Carrot root and DNA VCRU Bioinformatics USDA ARS Vegetable Crops Research Unit

This page was last updated on Sunday, 19-Jan-2020 08:56:31 CST

News and Updates

Feb 24, 2020
Blast+ updated from version 2.6.0+-1 to version 2.10.0+-4 on all servers
Jan 20, 2020
PHYLIP updated from version 3.696 to version 3.697 on all servers
Jan 19, 2020
VCF2Dis version 1.36 installed on Daucus server
Dec 11, 2019
Beagle updated from version 4.1 to version 5.1 on all servers
beagle-lib updated to commit 4056cfb on all servers
Dec 2, 2019
MUMmer updated from version 3.23 to version 4.0.0beta2 on all servers
Nov 21, 2019
the GATK updated from version 4.0.7.0 to version 4.1.4.0 on all servers
Nov 15, 2019
ABySS upgraded to version 2.1.5 on all servers
Nov 14, 2019
DISCOVARdenovo container installed in daucus server
Sep 25, 2019
RAxML installed/updated to version 8.2.12 on pickle server
Aug 26, 2019
MSMS version 3.2rc-b163 installed on carrot server
smc++ version ? installed on carrot server
Jul 3, 2019
Delly updated from version 0.7.6 to version 0.8.1 on all servers
Jun 25, 2019
Samtools, BCFtools, HTSlib updated from version 1.7 to versions 1.9 on all servers
Mar 8, 2019
Introgression Browser installed on pickle server
Feb 13, 2019
Roche 454 software version 3.0 installed on pickle server
Sep 29, 2018
Maker 2.31.10 installed on pickle server
Sep 18, 2018
Stacks updated from version 1.41 to version 2.2 on all servers
Aug 12, 2018
the GATK updated from version 4.0.4.0 to version 4.0.7.0 on all servers
Jul 11, 2018
FastQC version v0.11.7 installed on all servers
RepeatExplorer update to 2017-12-12 10bea50 version on carrot server
Jun 25, 2018
Circos updated from version 0.69-3 to 0.69-6 on all servers
Jun 10, 2018
rclone version 1.41 installed on all servers
May 11, 2018
the GATK updated from version 4.0.3.0 to version 4.0.4.0 on all servers
May 4, 2018
paup updated from version 4.0a159 to version 4.0a161 on all servers except cuke
Apr 25, 2018
the GATK updated from version 4.0.1.0 to version 4.0.3.0 on all servers
BWA updated from version 0.7.15 to version 0.7.17 on all servers
Apr 24, 2018
Interproscan version 5.28-67.0 with panther version 12.0 installed on pickle server
Apr 23, 2018
Blast2GO version 5.0.22 installed on pickle server
Mar 26, 2018
minimap2 version 2.9-r753-dirty installed on all servers
Mar 14, 2018
Samtools, BCFtools, HTSlib updated from version 1.3.x to versions 1.7 on all servers
As of this version the 1.x series is the default, to run the old 0.x series type export PATH="/usr/local/bin:$PATH"
SMRT Link version 5.0.1.9585 installed on daucus server
Mar 6, 2018
VSEARCH version 2.7.1 installed on all servers
GBS-SNP-CROP version 3.0 installed on daucus server
Mar 5, 2018
Pear version 0.9.11 installed on daucus server
Feb 1, 2018
the GATK updated from version 3.7 to version 4.0.1.0 on all servers
Jan 9, 2018
admixture version 1.3.0 Nov. 28, 2015 installed on all servers
Dec 6, 2017
XPCLR version 1.0 installed on all servers
Dec 1, 2017
RAxML installed/updated to version 8.2.11 on all servers
paup updated from version 4.0a152 to version 4.0a159 on all servers except cuke
Nov 5, 2017
HiC-Pro version 2.9.0 commit 8c98a2d installed on pickle server
Oct 22, 2017
augustus version 3.3 installed on carrot and pickle servers
BUSCO version 3.0.2b installed on carrot and pickle servers
HMMER updated from version 3.1b1 to version 3.1b2 on all servers
Oct 12, 2017
LinkImpute version 1.1 and LinkImputeR version 1.1.1 installed on all servers
Oct 9, 2017
alpha-CENTAURI version 0.2 commit 6a8659c on Oct 7, 2015 installed on all servers
telomerecat version 3.1.2 installed on all servers except cucumber
Sep 27, 2017
Tassel updated from version 5.2.31 October 20, 2016 to version 5.2.39 September 7, 2017 on all servers
Aug 13, 2017
muscle version 3.8.1551 - July 12, 2014 installed on all servers (but not default version)
Jul 11, 2017
EDirect version 7.00 installed on all servers
Jul 3, 2017
SRA Toolkit updated from version 2.8.0 to version 2.8.2-1 on all servers
Jun 27, 2017
canu version 1.5 installed on daucus server only
May 11, 2017
Organelle_PBA version 848c3ce on Oct 10, 2016 installed on pickle server only
May 7, 2017
ASCIIGenome version 1.6.0 installed on all servers
May 6, 2017
TICR installed on all servers
May 5, 2017
QMCN Quartet MaxCut version 2012-10-17 installed on all servers
Apr 19, 2017
paup version 4.0a152 installed on all servers except cuke, vaccinium
Apr 9, 2017
BEAGLE (beagle-lib) version commit 6ba09fa on Aug 31, 2016 installed on all servers
Beast BEAST version 1.8.4 installed on all servers
Mar 30, 2017
Pophelper version 2.0.0 installed on all servers
Mar 24, 2017
LASTZ version 1.04.00 installed on all servers
Mar 15, 2017
BUCKy installed/updated from version 1.4.2 to version 1.4.4 on all servers
MrBayes version 3.2.6 installed on all servers
Mar 8, 2017
Bowtie 2 updated from version 2.2.9 to version 2.3.1 on all servers
Mar 7, 2017
sprai version 0.9.9.23 installed on all servers
SSPACE-LongRead version 1-1 installed on all servers
Feb 6, 2017
BLAST+ updated from version 2.2.30 to version 2.6.0 (build Dec  7, 2016) on all servers
Jan 27, 2017
FigTree version 1.4.3 installed on all servers
The GATK updated from version 3.6 to version 3.7 on all servers
RAxML 8.2.9 installed on carrot server only, version on daucus unchanged
Jan 27, 2017
vg version v1.4.0-2109-g6863e98 2017-01-25 installed on carrot server only
Jan 26, 2017
fcGENE version 1.0.7 installed on all servers
MEGA2 version 4.9.1 installed on all servers
Jan 25, 2017
Bandage version 0.8.1 installed on all servers
MEGAHIT version 1.1.1 installed on all servers
Jan 11, 2017
ALLMAPS version 0.6.9 installed on all servers
Jan 4, 2017
mrsFAST version 3.4.0 32dda6a Nov 16, 2016 installed on all servers
RAPTR-SV version 0.0.15 Jun 8, 2015 installed on all servers
Dec 30, 2016
MELT version 2.0.2 installed on all servers
Dec 29, 2016
dd_detection Version 0.2.5, June 4 2013 commit 1bc2eb8 2015-10-08 installed on all servers
Dec 23, 2016
cutadapt version 1.12 installed on all servers
Newick Utilities version 1.6 disabled-extra (2011-11-23) installed on all servers
R is now version 3.3.2 (2016-10-31) "Sincere Pumpkin Patch" on all servers except cucumber where it is 3.2.5 (2016-04-14) "Very, Very Secure Dishes"
RepeatExplorer updated/installed to version 2016-08-22 fd28551 on all servers
Dec 20, 2016
TreeGraph2 version 2.11.1-654_beta installed on all servers
Dec 15, 2016
BBMap updated from version 36.59 to version 36.71 on all servers
Dec 14, 2016
PHYLIP version 3.696 installed on all servers
SNPhylo version 20160204 installed on all servers except cucumber and vaccinium
Dec 12, 2016
Pilon version 1.21 installed on all servers
Dec 8, 2016
MAFFT version 7.305 installed on all servers
Dec 6, 2016
GramAlign version 3_00 installed on all servers
Kalign version 2.04 installed on all servers
Dec 2, 2016
Artemis version 16.0.11 installed on all servers
Dec 1, 2016
plink 1.90 beta 3.44 161201 Nov. 17, 2016 installed on all servers
Nov 27, 2016
REAPR installed|updated from version v1.0.16 July 12, 2013 to version v1.0.18 Feb. 23, 2015 on all servers
Nov 22, 2016
Clustal Omega updated from version 1.2.0 to version 1.2.3 on all servers
distruct version 1.1 now installed on all servers
Nov 20, 2016
FASTA updated from version 36.3.6d (12/12/2013) to version 36.3.8e (9/30/2016) on all servers
RepeatMasker updated to version 4-0-6 with RMLibrary Version|Repbase Version 20160829 and DFAM Library Version Dfam_2.0 on all servers
Nov 19, 2016
bfast version 0.7.0b installed on all servers
DeconSeq standalone version 0.4.3 now installed on all servers
Nov 18, 2016
RSEM updated to version 1.3.0 on all servers
Nov 14, 2016
Haploview version 4.2 installed on all servers
MEGA updated from version 7.00 to version 7.0.20-Proto | MEGA-CC 7.0.20(7161007-x86_64) on all servers
Primer3 updated from version 2.3.6 to version 2.3.7 on all servers
Nov 13, 2016
breakdancer updated from version 1.4.4-dirty (commit ad4dca4-dirty) to version 1.4.5-unstable-66-4e44b43-dirty (commit 4e44b43-dirty) Nov 23, 2015
fastq-tools updated from version 89b060d (0.7) to version 79dbc8c (0.8) on all servers
Trans-ABySS installed/updated from version 1.4.8 to version 1.5.5 on all servers
Nov 12, 2016
BBMap updated from version 33.13_java7 to version 36.59 on all servers
Beagle updated from version 4.0 (r1399) to version 4.1 (27Jul16.86a) on all servers
Delly updated from version 0.7.2 to version 0.7.6 on all servers
GenomeTools updated from version 1.5.7 to version 1.5.9 on all servers
Jellyfish updated from version 2.2.5 to version 2.2.6 on all servers
Lumpy updated from version 0.2.12 to version 0.2.13 on all servers
MView updated from version 1.56 to version 1.60.1 on all servers
NCBI C++ Toolkit version 12_0_0 installed on all servers
samblaster updated from version 0.1.22 3fe403f Jun 18, 2015 to version 0.1.23 dadeb37 Sept. 22, 2016 on all servers
SRA Toolkit updated from version 2.3.5-2 to version 2.8.0 on all servers
STAR updated from version version 2.5.0a to version 2.5.2b on all servers
Nov 11, 2016
bamtools updated from version 2.3.0 to version 2.4.1 on all servers
Bowtie 2 updated from version 2.2.8 to version 2.2.9 on all servers
BWA updated from version 0.7.13 to version 0.7.15 on all servers
Mauve updated from version 2.3.1 (11/11/2009) to version snapshot_2015-02-13 on all servers
Picard updated from version 1.127 to 2.7.1 on all servers
Samtools, BCFtools, HTSlib updated from version 1.3 to versions 1.3.1 1.3.1 1.3.2 on all servers
Tassel updated from version 5.2.26 June 16, 2016 to version 5.2.31 October 20, 2016 on all servers
Nov 10, 2016
Bioconductor updated on all servers
BEDOPS updated to version 2.4.20.v2 on all servers
BEDTools updated to version 2.26.0 on all servers
Circos updated to version 0.69-3 and circos-tools to version 0.22 on all servers
tbl2asn updated from version 24.3 to version 25.3 on all servers
Trimmomatic updated from version 0.32 to version 0.36 on all servers
tRNAscan-SE version 1.3.1 installed on all servers
Nov 9, 2016
ABySS updated to version 2.0.2 on all servers
IGV updated to version 2.3.88 on all servers
Tablet updated to version 1.16.09.06 on all servers
Nov 8, 2016
HTSeq updated to version 0.6.1p1 on all servers
Nov 7, 2016
gridss version 0.11.7 installed on all servers
Sep 1, 2016
ABySS updated to version 2.0.0 on all servers except carrot
Aug 26, 2016
bam-readcount version 0.7.4-unstable-37-c75d864-dirty Aug. 10, 2016 installed on all servers
Aug 23, 2016
freebayes version v1.0.2-33-gdbb6160 Jun 23, 2016 installed on all servers except cranberry
Aug 5, 2016
Sequin updated from version 13.70 to 15.10 on all servers
Jul 29, 2016
Default Oracle java version on all servers is now 1.8
The GATK updated from version 3.5 to version 3.6 on all servers
Jul 10, 2016
Trinity updated from version 2.1.1 to version 2.2.0 on all servers
Jul 6, 2016
Mesquite updated to version 3.10 on all servers
Jul 1, 2016
AliView version 1.18 installed on all servers
Jun 27, 2016
Stacks updated from version 1.35 to version 1.41 on all servers
Jun 21, 2016
Tassel5 updated to version 5.2.26 on all servers
May 20, 2016
PipMaker version 2011-08-12-01 installed on web server
May 5, 2016
fastStructure updated from version 01e0183829 Nov. 13, 2014 to version e47212f Mar. 19, 2015 on all servers
Apr 21, 2016
Jellyfish updated from version 2.1.4 to version 2.2.5 on all servers
Apr 12, 2016
TopHat updated from version 2.1.0 to version 2.1.1 on all servers
Bowtie 2 updated from version 2.2.5 to version 2.2.8 on all servers
Apr 2, 2016
MEME suite updated from version 4.9.1_1 to 4.11.1 on all servers
Mar 26, 2016
The GATK updated from version 3.3-0 to version 3.5 on all servers
Platanus Genome Assembler updated from version 1.2.1 to 1.2.4 on all servers
Mar 23, 2016
Celera updated to version 8.3rc2 on all servers
Feb 24, 2016
BWA updated to version 0.7.13 on all servers
Feb 16, 2016
Samtools, BCFtools, HTSlib updated to version 1.3 on all servers
Pindel updated to version 0.2.5b8, 20151210 on all servers
Jan 21, 2016
IGV updated to version 2.3.68 on all servers
Jan 14, 2016
fastQValidator version 0.1.1a installed on all servers
Jan 10, 2016
Annovar version 2015Dec14 installed on all servers
Jan 8, 2016
SignalP version 4.1c installed on all servers
tmhmm version 2.0c installed on all servers
RNAmmer version 1.2 installed on all servers
Jan 7, 2016
Trinity updated to version 2.1.1 on all servers
Trinotate version 2.0.2 installed on all servers
iCommands updated|installed to version 4.1.7 on all servers except carrot
Jan 1, 2016
samblaster version 0.1.22 3fe403f Jun 18, 2015 installed on all servers
Dec 31, 2015
SplitsTree4 version 4_14_2 installed on all servers
svtyper version f1e2f59 Oct. 5, 2015 installed on all servers
Dec 29, 2015
Delly version 0.7.2 installed on all servers
Lumpy version 0.2.12 installed on all servers
Dec 17, 2015
iBLUP version 20 May, 2013 installed on all servers
Dec 5, 2015
blobology installed on carrot and daucus servers
DeconSeq standalone version 0.4.3 installed on daucus server, earlier was on carrot server only
Dec 4, 2015
vcftools updated to version 0.1.14 on all servers
Dec 2, 2015
Stacks updated to version 1.35 on all servers
Dec 1, 2015
gasv version Release_Oct1_2013 installed on carrot and daucus servers
Nov 27, 2015
SNAP on carrot server updated to version 2013-11-29
Nov 27, 2015
Maker on carrot server updated to version 2.31.8
Nov 25, 2015
GenomeTools on carrot server updated to version 1.5.7
Nov 24, 2015
SpliceGrapher installed/updated to version 0.2.5 on all servers
Nov 23, 2015
TransDecoder version 2.0.1 installed on all servers
Nov 18, 2015
IGV updated to version 2.3.65 on all servers
Nov 10, 2015
STAR updated to version 2.5.0a on all servers
Oct 29, 2015
Structure Harvester version "structureHarvester.py v0.6.94 July 2014 core vA.2 July 2014" installed on all servers
Oct 27, 2015
Structure version 2.3.4 is now installed on all servers
Oct 23, 2015
Tassel5 updated to version 5.2.16 on all servers
Sep 25, 2015
RAxML version 8.2.3 installed on daucus server
Sep 7, 2015
GMAP and GSNAP updated to version 2015-07-23 on all servers
Aug 27, 2015
ABySS updated to version 1.9.0 on all servers except carrot
Aug 26, 2015
Haploview installed on daucus server
Circos updated to version 0.67-7 and circos-tools to version 0.21 on all servers
Aug 10, 2015
Stacks updated to version 1.34 on all servers
July 16, 2015
Primer3 versions 2.3.6 and 1.1.4 are now installed on all servers
RepeatMasker version 4-0-5 with repeatmaskerlibraries-20140131 is now installed on all servers
July 6, 2015
Bowtie updated to versions 1.1.2 and 2.2.5 on all servers
TopHat updated to version 2.1.0 on all servers
June 23, 2015
Beagle 4.0 (r1399) installed on all servers
May 24, 2015
Zorro version 2.2 installed on all servers
May 18, 2015
Sequin updated to version 13.70 on all servers
May 15, 2015
Stacks updated to version 1.30 on all servers
May 5, 2015
tbl2asn version 24.3 Apr 29, 2015 installed on all servers
Apr 22, 2015
MEGA-CC version 7.00 installed on all servers
Apr 3, 2015
cdbfasta / cdbyank version 2010-07-22 (re)installed on all servers
seqtk version 5e1e8dbd50 1.0-r82-dirty 2015-03-24 installed on all servers
Mar 6, 2015
RATT revision 18 installed on all servers
Feb 17, 2015
FUNC version 0.4.7 installed on daucus server
Feb 16, 2015
SSPACE standard version 3.0 updated/installed on all servers
GapFiller version v1-10 installed on all servers
Feb 13, 2015
SAMtools updated to version 1.2 on all servers, but due to some compatibility problems with the new series of versions, the default version has been reverted to 0.1.19
Feb 11, 2015
BEDOPS updated to version 2.4.8 on all servers
BEDTools updated to version 2.22.1 on all servers
Feb 7, 2015
DAGchainer version r02-06-2008 installed on all servers
Feb 6, 2015
SOAP GapCloser version 1.12-r6 2013-01-11 installed on all servers
Jan 30, 2015
MCScanX and MCScanX-transposed are now installed on all servers
Jan 28, 2015
FGAP version 1_7 installed on all servers
Jan 26, 2015
MCL version 14-137 and OrthoMCL version 2.0.9 installed on all servers
Jan 2, 2015
Price updated to version 1.2 (140408) on all servers
Dec 29, 2014
BWA updated to version 0.7.12 on all servers
Tablet updated to version 1.14.10.21 on all servers
Dec 22, 2014
Tassel4 updated to version 4.3.13 on all servers
Tassel5 version 5.2.2 installed on all servers
Dec 21, 2014
Jellyfish updated/installed to version 2.1.4 on all servers, and jellyfish version 1.1.11 executable is still available as jellyfish1 on all servers
Bowtie updated to versions 1.1.1 and 2.2.4 on all servers
GMAP and GSNAP updated to version 2014-12-16 on all servers
Picard updated to version 1.127 on all servers
HMMER version 3.1b1 installed on all servers
Dec 20, 2014
Velvet updated to version 1.2.10 on all servers (Oases is still at version 0.2.08)
Dec 17, 2014
BLAST+ updated to version 2.2.30 on all servers
Dec 16, 2014
samtools updated to version 1.1 on all servers
FASTX-Toolkit updated to version 0.0.14 on all servers
Dec 15, 2014
New pickle server initial install
Dec 13, 2014
gvcftools version 0.16 installed on all servers
Dec 5, 2014
The GATK updated to version 3.3-0 on all servers
Nov 28, 2014
Tablet updated to version 1_14_10_21 on all servers
jvarkit installed on daucus server to install SAM4WebLogo
Nov 27, 2014
GenomeTools version 1.4.2 now installed on all servers
Nov 26, 2014
weblogo version 3.4 installed on all servers
Nov 22, 2014
PlantTFcat backend pipeline installed on all servers
Nov 20, 2014
InterProScan 5.7-48.0 and Panther 9.0 installed on daucus server
Nov 15, 2014
plink installed on all servers
Nov 13, 2014
fastStructure installed on all servers
Nov 4, 2014
IGV updated to version 2.3.40 on all servers
matrix2png version 1.2.2 installed on all servers
Nov 1, 2014
Celera updated to version 8.2beta on all servers
Oct 29, 2014
Mesquite installed on all servers
Oct 15, 2014
The GATK updated to version 3.2-2 on all servers
Sep 17, 2014
khmer installed on daucus server
Sep 7, 2014
SOAPdenovo2 updated to version 2.04 r204 on all servers
Aug 30, 2014
RSEM updated to version 1.2.16 on all servers
bioconductor updated on all servers, and R versions are now all ≥3
Picard updated to version 1.119 on all servers
Aug 28, 2014
Stacks updated to version 1.20 on all servers
Tassel 4 standalone updated to version 4.3.11 July 24, 2014 on all servers
Aug 26, 2014
GMAP and GSNAP updated to version 2014-08-20 on all servers
ABySS updated to version 1.5.2 on all servers
SSAHA2 updated/installed to version v2.5.5 on all servers
SRA Toolkit updated to version 2.3.5-2 on all servers
Aug 23, 2014
Trinity updated to version r20140717 on all servers
Aug 18, 2014
fastq-tools installed on all servers
Aug 2, 2014
BWA updated to version 0.7.10 on all servers
Aug 1, 2014
Bowtie1 updated to version 1.1.0 on all servers
Bowtie2 updated to version 2.2.3 on all servers
TopHat updated to version 2.0.12 on all servers
Cufflinks updated to version 2.2.1 on all servers
Blast+ updated to version 2.2.29 on all servers
Jul 30, 2014
BBMap version 33.13_java7 installed on all servers
vcftools updated to version 0.1.12a on all servers
Jul 21, 2014
SMRT Analysis version 2.2 virtual machine installed on vaccinium server
Jul 17, 2014
PBSIM version 1.0.3 installed on all servers
Jul 15, 2014
BEDtools updated to version 2.20.1 on all servers
wgsim version 0.3.1-r13 installed on all servers
PfamScan installed on carrot server only
Jul 9, 2014
Jellyfish updated to version 2.1.3 on all servers
Jul 7, 2014
ABySS updated to version 1.5.1 on all servers
Jul 2, 2014
Platanus Genome Assembler version 1.2.1 installed on all servers
Mira updated to version 4.0.2 on all servers
Jun 27, 2014
MCScanX and MCScanX-transposed installed, carrot server only
Jun 26, 2014
MAKER (carrot server only) updated to version 2.31.6
May 29, 2014
BEDOPS version 2.4.2 installed on all servers
May 23, 2014
BWA updated to version 0.7.9a on all servers
May 14, 2014
Tassel 4 standalone updated to current version on all servers
May 10, 2014
Picard updated to version 1.113 on all servers
May 9, 2014
Stacks updated to version 1.19 on all servers
Apr 15, 2014
Structure version 2.3.4 installed on cucumber server, carrot updated to same version
Apr 6, 2014
MView version 1.56 installed on all servers
Mar 31, 2014
Cufflinks updated to version 2.2.0 on all servers
Mar 26, 2014
PAGIT 1 installed on all remaining servers
Mar 24, 2014
InterProScan version 5.3-46.0 installed on vaccinium and carrot servers only
Mar 23, 2014
MUSCLE versions 3.8.31b and 3.8.425 installed on all servers, although version 3.8.31 is still the default version.
MEME version 4.9.1_1 Nov 11, 2013 installed on all servers except cranberry
Mar 19, 2014
GFF2PS version 0.98d installed on carrot server only
Mar 18, 2014
The GATK updated to version 3.1-1 on all servers
Mar 17, 2014
RepeatExplorer updated to version 2014-03-14 on carrot server only
Mar 13, 2014
TopHat updated to version 2.0.11 on all servers
Mar 12, 2014
AMOS updated to version 3.1.0rc2 on carrot, daucus servers
Feb 18, 2014
ABySS updated to version 1.3.7 on all servers
Feb 17, 2014
The GATK updated to version 2.8-1 on all servers
Feb 12, 2014
MAKER (carrot server only) updated to version 2.31
Feb 8, 2014
Celera updated to version 8.1 on all servers
Jan 23, 2014
iTAK version v1.2 Aug-26-2011 installed on all servers
Jan 22, 2014
RepeatExplorer installed on carrot server only
Jan 21, 2014
FASTA version 36.3.6d (12/12/2013) installed on all servers
Jan 16, 2014
bcftools updated to version 0.2.0-rc5-60 on all servers
Jan 13, 2014
Mira updated to version 4.0rc5 on all servers
Jan 12, 2014
Bowtie1 updated to version 1.0.0 on all servers
Jan 10, 2014
Trimmomatic installed/updated to version 0.32 on all servers
PRINSEQ updated to version 0.20.4 on all servers
Jan 2, 2014
VCFtools version 0.1.11 installed on all servers
Jan 1, 2014
Picard updated to version 1.105 on all servers
Dec 26, 2013
SAMStat version 1.09 installed on all servers
Dec 20, 2013
SOAPsnp version 1.03 installed on all servers
SOAPindel version 2.1.4.8 installed on all servers
Dec 8, 2013
Celera version 8.0 installed/updated on all servers
Dec 6, 2013
ESTScan version 3.0.3 installed on carrot server only
Nov 30, 2013
Picard updated to version 1.103 2013/11/18 on all servers
Nov 26, 2013
breakdancer version 1.4.4-dirty (commit ad4dca4-dirty) installed on Vaccinium server, and Carrot server updated to this version
Nov 21, 2013
cnD version 1.3 installed on all servers
Nov 20, 2013
tabix version 0.2.4 (10 April, 2011) installed on all servers
SNP-o-matic version revision 14 installed on all servers
SVMerge version 1.2r37 installed on all servers
REAPR version v1.0.16 July 12, 2013 installed on carrot server only
Nov 14, 2013
DeconSeq standalone version 0.4.3 installed on carrot server only
Nov 7, 2013
FASTX-Toolkit updated to version 0.0.13.2 26-Apr-2012 on all servers
bamtools version 2.3.0 installed on all servers
Nov 6, 2013
CD-HIT updated to version 4.6.1-2012-08-27 on all servers
Nov 2, 2013
readDepth v0.9.8.4 installed on carrot server
Nov 1, 2013
Pindel version 0.2.4 installed on all servers
Oct 31, 2013
svdetection version 2012/07/11 installed on all servers
Oct 29, 2013
Picard updated to version 1.101 2013/10/21 on all servers
SVDetect version r0.8b 2013/01/23 installed on all servers
Oct 29, 2013
HTSeq version 0.5.4p5 2013/10/10 installed on all servers
Oct 23, 2013
BLAST+ updated to version 2.2.28 on all servers
BWA updated to version 0.7.5a-r405 on all servers
Oct 17, 2013
ABySS updated to version 1.3.6 on all servers
Oct 15, 2013
MIRA updated to version 4.0rc4 on all servers
Sep 19, 2013
breakdancer version 1.3.6 installed, Carrot server only
TopHat updated to version 2.0.9 all servers
Cufflinks updated to version 2.1.1 all servers
Sep 13, 2013
breakdancer versions 1.1 and 1.0 installed, Carrot server only
Sep 11, 2013
PRINSEQ version 0.20.3 installed all servers
Aug 28, 2013
gce installed, Carrot server only
Aug 26, 2013
SOAPec installed, Carrot server only
Aug 21, 2013
Jellyfish updated to version 1.1.11 on all servers
Aug 18, 2013
Trinity updated to version 2013_08_14 on all servers
Jul 24, 2013
Clustal Omega version 1.2.0 installed on all servers
Jul 18, 2013
Samtools updated to version 0.1.19 on carrot
Jul 8, 2013
BLASR installed on carrot and vaccinium
Jul 1, 2013
MITOFY public web server installed
Jun 30, 2013
Celera development version compiled with Pac-Bio support on carrot server
A virtual machine installed with the Pac-Bio SMRT software and PBJelly
Jun 27, 2013
MCScan version 0.8 installed on all servers
Jun 12, 2013
PRICE updated/installed to version 1.0.1 on all servers
Jun 5, 2013
Circos updated/installed to version 0.64 on all servers + web server, including circos-tools version 0.16-2
May 23, 2013
Picard version 1.92 installed on all servers
May 21, 2013
The GATK version 2.5-2 installed on all servers
May 20, 2013
Tablet updated to version 1_13_05_17 on all servers
May 11, 2013
Bowtie2 updated to version 2.1.0 on all servers
May 4, 2013
SHRiMP version 2.2.3 installed/updated on all servers
May 3, 2013
BUCKy version 1.4.2 installed on all servers
Harry Plotter installed on all servers
Apr 15, 2013
PAGIT 1 installed on carrot server
Apr 13, 2013
SyMAP 4.0 installed on carrot server
Apr 9, 2013
DiffSplice 0.1.1 installed on all servers
Apr 8, 2013
STAR 2.3.0.e installed on all servers
subread 1.3.1 installed on all servers
Apr 7, 2013
SpliceGrapher 0.2.2 installed on all servers
Mar 11, 2013
Tablet updated to version 1_12_12_05 on all servers
Roche GSAssembler/Newbler updated to version 2.8 on all servers (old versions also still available)
Legacy blast executables version 2.26 are installed on all servers, in /usr/local/bin/legacyblast/, for programs such as FPC that don't support the newer blast+ version.
Mar 10, 2013
FPC version 9.4 installed on all servers
Blast+ updated to version 2.27 on all servers
Mar 4, 2013
EBSeq version 1.1.6 installed on all servers
Feb 28, 2013
Trinity updated to version 2013-02-25 on all servers;
cdbfasta / cdbyank version 2010-07-22 installed on all servers
Feb 10, 2013
PANDAseq installed on all servers
Feb 9, 2013
Biopieces installed on all servers
Bioconductor packages edgeR and DESeq (used by Trinity) added to all servers
Installed GMAP and GSNAP version 2013-02-05 on all servers
BLAT updated to version 35
Feb 7, 2013
Trimmomatic version 0.22 installed on all servers
Jan 29, 2013
Bowtie2 updated to version 2.0.6 on all servers
Jan 28, 2013
RSEM 1.2.3 installed on all servers
Jan 21, 2013
Tophat updated to version 2.0.6 on all servers
Jan 20, 2013
Bowtie (Bowtie 1, not Bowtie 2) updated to version 0.12.9 on all servers and is now in the default path for all users. This is required by Trinity.
Jan 19, 2013
Sequin updated to version 12.30 on all servers
Jan 16, 2013
Trinity updated to version 2012-10-05 on all servers
Jan 14, 2013
MIRA updated to version 3.4.1.1 on all servers
Jan 4, 2013
Short Read Archive Toolkit installed on all servers
Dec 2, 2012
GenomeTools installed (Carrot and Cucumber)
Nov 29, 2012
MAKER installed (Carrot only)
Nov 29, 2012
SNAP installed (Carrot only)
Nov 29, 2012
Augustus installed (Carrot only)
Nov 29, 2012
Exonerate installed (Carrot only)
Nov 26, 2012
Sabre installed (Carrot only)
Oct 15, 2012
Stacks updated to version 0.9999
Aug 29, 2012
JoinMap 3.0 installed
Aug 28, 2012
Mira installed/updated to version 3.9.4
MUMmer installed/updated to version 3.23
Installed AMOS version 3.1.0
Installed/updated Consed version 23.0
Aug 27, 2012
Genomica installed version 3.040710
Aug 26, 2012
BLAT installed/updated to version 3.5,
pysam installed/updated to version 0.6,
Biopython installed/updated 1.59-1(Carrot) 1.54-1(Cranberry) 1.58-1(Cucumber),
BWA installed/updated to version 0.6.2,
Trans-ABySS installed/updated to version 1.3.2,
Installed Bambino version 1.05
Aug 25, 2012
ABySS updated to latest version 1.3.4
Aug 24, 2012
Velvet and Oases updated to latest versions 1.2.07 and 0.2.08
Aug 23, 2012
Stacks Version 0.9996 installed (Carrot server only for now)
Aug 22, 2012
Circos updated to version 0.62-1
Installed/updated TASSEL3 and TASSEL4 to versions 3.0.101 and 4.0.4
Aug 21, 2012
Installed Bioconductor
Aug 19, 2012
Installed BAMseek version 2011July24
Seqmonk version 0.21.0
MochiView v1.45
Aug 19, 2012
Installed Savant Genome Browser version 2.0.3
updated IGV Integrative Genomics Viewer to version 2.1.21 (2541)
Aug 18, 2012
Installed/updated ABySS Explorer version 1.3.4
updated Tablet to version 1.12.03.26; 26th March 2012
Aug 3, 2012
Installed version 2.7 of the Roche gsAssembler/Newbler etc. software

Index of Installed Programs

= installed on cucumber server
= installed on cranberry server
= installed on carrot server
= installed on vaccinium server
= installed on daucus server
= installed on pickle server

List of Installed Programs

ABySS - A parallel assembler for short read sequence data

ABySS Logo

http://www.bcgsc.ca/platform/bioinfo/software/abyss

ABySS Users Forum Archive

ABySS Wiki

Original Publication

Other Publications using ABySS

Installation notes

ABySS-Explorer - Novel graph-based representation of sequence assembly

http://www.bcgsc.ca/platform/bioinfo/software/abyss-explorer/

v1_3_0_user_manual.pdf (local copy)

ABySS-Explorer is an interactive Java application that employs a novel graph-based representation to display a sequence assembly and associated meta data. The tool was designed with the ABySS sequence assembler in mind and was motivated by the need to examine assembly structure, in particular contig connectivity and supporting paired-end read relationships.

Publications:

ABySS-Explorer 1.0 source code link

Installation notes

Trans-ABySS - Analyze ABySS multi-k-assembled shotgun transcriptome data

http://www.bcgsc.ca/platform/bioinfo/software/trans-abyss

Installation notes

admixture - Fast ancestry estimation

http://www.ormbunkar.se/aliview/

A local copy of the manual: admixture-manual.pdf

Installation notes

AliView - Lightweight alignment viewer and editor

http://www.ormbunkar.se/aliview/

Installation notes

ALLMAPS -

https://github.com/tanghaibao/jcvi/wiki/ALLMAPS

Installation notes

alpha-CENTAURI - Mine alpha satellites and their higher-order structures in sequence data

https://github.com/volkansevim/alpha-CENTAURI

Installation notes

AMOS - A Modular, Open-Source whole genome assembler

http://sourceforge.net/apps/mediawiki/amos/

BAMBUS2 is part of AMOS

Installation notes

Annovar - Functionally annotate genetic variants

http://annovar.openbioinformatics.org/

Installation notes

Artemis - DNA sequence viewer and annotation tool

http://www.sanger.ac.uk/science/tools/artemis

Artemis Manual

Installation notes

ASCIIGenome - Text only genome viewer

https://github.com/dariober/ASCIIGenome

Documentation

Installation notes

Augustus - A program that predicts genes in eukaryotic genomic sequences

http://bioinf.uni-greifswald.de/augustus/

Augustus config directory is set to AUGUSTUS_CONFIG_PATH=/etc/augustusconfig

Local copies of documentation

Installation notes

Bambino - A graphical viewer and variant detector for NGS files in SAM/BAM format

https://cgwb.nci.nih.gov/goldenPath/bamview/documentation/index.html
Java Web Launch at https://cgwb.nci.nih.gov/goldenPath/bamview/documentation/index.html#launch
or NIH Web Implementation https://cgwb.nci.nih.gov/cgi-bin/bambino

If running from the command line, the path to the Java .jar file is /usr/local/bin/bambino_bundle.jar

BAMseek - A Large File Viewer for BAM and SAM alignment files

http://code.google.com/p/bamseek/

http://code.google.com/p/bamseek/wiki/bamseek

The program is available to all users in the "Bioinformatics" menu

bam-readcount - Count DNA sequence reads in BAM files

https://github.com/pezmaster31/bamtools

Installation notes

bamtools - C++ API & command-line toolkit for working with BAM data

https://github.com/pezmaster31/bamtools

Using the toolkit (pdf)

Installation notes

Bandage - a Bioinformatics Application for Navigating De novo Assembly Graphs Easily

http://rrwick.github.io/Bandage/

Wiki

Installation notes

BAPS - Bayesian Analysis of Population Structure

http://web.abo.fi/fak/mnf/mate/jc/software/baps.html

The program is available to all users in the "Bioinformatics" menu

Black box programs - Programs Doug has written

https://github.com/dsenalik/bb

Type bb to get a list of the "black box" programs currently available.
These are all Perl programs that Doug has written to do useful stuff.

bb.454contigannotate
   Add some extra information to the contig FASTA file, and
   optionally generate statistics files
bb.454contignet
   Create a network of all contigs connected to a contig
bb.454singletons
   Create a FASTA and a FASTQ file of all singletons (i.e. good
   but not assembled reads)
bb.454summarizer
   Summarize Roche 454 Assembly files, creating a brief overall
   summary file
bb.sff2fastq
   Shell script to convert Roche 454 sff file to FASTQ file,
   retaining all information in the header (sff2fastq is way
   faster, but loses this information)

BBMap - Short read aligner, and other bioinformatic tools

http://bbmap.sourceforge.net/

Here is a local copy of the included readme.txt file, or see the current version at http://sourceforge.net/projects/bbmap/files/.

Installation notes

Beagle - genotype calling, genotype phasing, imputation of ungenotyped markers, and identity-by-descent segment detection

http://faculty.washington.edu/browning/beagle/beagle.html

A wrapper program beagle can be used to run the Java .jar file

Beagle version 4.0 documentation (Local copy)

Installation notes

BEAGLE (beagle-lib) - General purpose library for evaluating the likelihood of sequence evolution on trees

https://github.com/beagle-dev/beagle-lib

Installation notes

BEAST - Bayesian Evolutionary Analysis Sampling Trees

https://github.com/beast-dev/beast-mcmc

Documentation

Installation notes

BEDOPS - the fast, highly scalable and easily-parallelizable genome analysis toolkit

https://bedops.readthedocs.org/en/latest/

Usage Examples

Reference

Installation notes

BEDTools - A flexible suite of utilities for comparing genomic features

BEDTools Logo

https://github.com/arq5x/bedtools2

BEDTools Documentation

The command-line programs are available in the default PATH for all users

Installation notes

BFAST - Blat-like Fast Accurate Search Tool

http://sourceforge.net/apps/mediawiki/bfast

The command-line programs are available in the default PATH for all users

A local copy of the manual: bfast-book.pdf
and of the work flow: work-flow.pdf
and of the work flow in color space: work-flow-color.pdf

Installation notes

Bioconductor - Analysis and comprehension of high-throughput genomic data with R

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language

http://www.bioconductor.org/

The base Bioconductor packages are installed and available in the R environment

Installation notes

BioMart - Unified access to distributed research data

Installation notes

Biopieces - Biopieces is a bioinformatic framework of tools easily used and easily created

http://maasha.github.io/biopieces/

To use, you will have to

  1. Create directories in your home directory:
  2. Add the following text to the end of your .bashrc file:
    nano ~/.bashrc
    # biopieces
    export BP_DIR="/usr/local/bin/biopieces"  # Directory where biopieces are installed
    export BP_DATA="$HOME/biopiecesdata"	  # Contains genomic data etc.
    export BP_TMP="/tmp"                      # Required temporary directory.
    export BP_LOG="$HOME/logs/biopieceslog"   # Required log directory.
    
    if [ -f "$BP_DIR/bp_conf/bashrc" ]; then
        source "$BP_DIR/bp_conf/bashrc"
    fi

Installation notes

BLASR - Basic Local Alignment with Successive Refinement

http://bix.ucsd.edu/projects/blasr/

GitHub page

BLASR help output from blasr -h
BLASR help output from blasr -help

Installation notes

Blast2GO - Functional Annotation

Blast2GO Logo

The program is available to all users in the "Bioinformatics" menu

https://www.blast2go.com/

Online Manual

Installation notes

Obsolete: Installation notes for local Blast2GO database installation

blast Legacy version - Basic Local Alignment Search Tool

http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download

Installation notes

BLAST+ - Basic Local Alignment Search Tool

http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download

Installation notes

Blat - Fast alignment of similar sequences

References

The command-line programs are available in all users' path:

------- Blat and related utilities -------------
blat - Fast alignment of similar sequences. (license needed for commercial use)
psLayout - Fast program to find largish DNA overlaps. (commercial license)
pslFilter - filter out psl file
pslPretty - Convert PSL to human readable output
pslReps - Find repeats and best or near best in genome alignments.
pslSwap - Swap query and target in  PSL

Installation notes

blobology - Blobplots or Taxon-Annotated-GC-Coverage plots (TAGC plots)

https://github.com/blaxterlab/blobology

Installation notes

Bowtie - An ultrafast memory-efficient short read aligner

Bowtie Logo

Bowtie 1 is available in the default PATH for all users on all computers

Bowtie1 Installation notes

Bowtie 2 - An ultrafast memory-efficient short read aligner

Bowtie Logo

Bowtie 2 is available in the default PATH for all users on all computers

Bowtie2 Installation notes

breakdancer - genome-wide detection of structural variants from paired-end reads

https://github.com/genome/breakdancer

Brief description copied from the home page

BreakDancer-1.3.6, released under GPLv3, is a Cpp package that provides genome-wide detection of structural variants from next generation paired-end sequencing reads. It includes two complementary programs. BreakDancerMax predicts five types of structural variants: insertions, deletions, inversions, inter- and intra-chromosomal translocations from next-generation short paired-end sequencing reads using read pairs that are mapped with unexpected separation distances or orientation. BreakDancerMini focuses on detecting small indels (usually between 10bp and 100bp) using normally mapped read pairs. Please read our paper for detailed algorithmic description.
http://www.nature.com/nmeth/journal/v6/n9/abs/nmeth.1363.html

README version 1.4.1

Version 1.4.1 Installation notes

README version 1.1

Version 1.1 Installation notes

The programs are all in the default PATH for all users

BUCKy - A Program for Bayesian Concordance Analysis

http://www.stat.wisc.edu/~ane/bucky/index.html

http://dstats.net/download/http://www.stat.wisc.edu/~ane/bucky/v1.4/bucky_manual1.4.0.pdf

README file

Installation notes

BUSCO - Assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs

https://gitlab.com/ezlab/busco

The example configuration file, with paths updated appropriately, is
/usr/local/bin/busco/config/config.ini.default

BUSCO_v3_userguide.pdf (local copy)

Installation notes

BWA - Burrows-Wheeler Aligner

http://bio-bwa.sourceforge.net/

BWA Manual

The programs are available in the default PATH for all users, so just type bwa to use it

Installation notes

canu - A single molecule sequence assembler for genomes large and small

https://github.com/marbl/canu

Installation notes

CAP3 Sequence Assembly Program

http://seq.cs.iastate.edu/

Cap3 documentation page

A web server to run cap3 is available at http://deepc2.psi.iastate.edu/aat/cap/cap.html

Program parameters (obtained by running cap3 with no parameters)

cap3 is not currently in the default PATH, to use it type /usr/local/bin/CAP3/cap3

Documentation files included with CAP3

Installation notes

CarthaGène - A genetic/radiated hybrid mapping software

http://www.inra.fr/mia/T/CartaGene/

http://www.inra.fr/mia/T/CartaGene/

Installed to default PATH for all users, type carthagene to run.

CD-HIT - A program for clustering DNA/protein sequence database at high identity with tolerance

http://cd-hit.org/
download page is https://github.com/weizhongli/cdhit

Installed to default PATH for all users, type cd-hit, cd-hit-454, etc.

cdhit-user-guide.pdf

Installation notes

Complete list of CD-HIT programs:
cd-hit
cd-hit-est
cd-hit-2d
cd-hit-est-2d
cd-hit-div
cd-hit-454
cd-hit-2d-para.pl
cd-hit-div.pl
cd-hit-para.pl
clstr2tree.pl
clstr2txt.pl
clstr2xml.pl
clstr_cut.pl
clstr_merge_noorder.pl
clstr_merge.pl
clstr_quality_eval_by_link.pl
clstr_quality_eval.pl
clstr_reduce.pl
clstr_renumber.pl
clstr_rep.pl
clstr_reps_faa_rev.pl
clstr_rev.pl
clstr_select.pl
clstr_select_rep.pl
clstr_size_histogram.pl
clstr_size_stat.pl
clstr_sort_by.pl
clstr_sort_prot_by.pl
clstr_sql_tbl.pl
clstr_sql_tbl_sort.pl
make_multi_seq.pl
plot_2d.pl
plot_len1.pl
psi-cd-hit-2d-g1.pl
psi-cd-hit-2d.pl
psi-cd-hit-local.pl
psi-cd-hit.pl

Celera Assembler - A de novo whole-genome shotgun (WGS) DNA sequence assembler

Celera Assembler Home Page

The programs are available in all users' path, so just type the name of a program to run it, e.g. sffToCA or runCA

Version 6.1 Release Notes

Version 7.0 Release Notes

Version 8.0 Release Notes

Version 8.1 Release Notes

Installation notes

Installation notes for the development version, revision 4358, June 30, 2013

cdbfasta / cdbyank - Fasta file indexing and retrival tool

http://sourceforge.net/projects/cdbfasta/

README

cdbfasta_usage.html

Installation notes

Circos - Circular Visualization

http://circos.ca/

Installation notes

circos is in the default PATH for all users, circos-tools is not

There is a web site, Circoletto at http://bat.ina.certh.gr/tools/circoletto/ which implements a web interface to Circos

CLUMPP - Label switching and multimodality problems in population-genetic cluster analyses

http://www.stanford.edu/group/rosenberglab/clumpp.html

CLUMPP_Manual.pdf (local copy)

Clustal Omega - Multiple Sequence Alignment

Clustal Omega Logo

http://www.clustal.org/omega/

The program is in the default PATH for all users, type clustalo to run

Clustal Omega documentation

This program can use multiple processors, use the --threads= parameter

Installation notes

ClustalW2 - Multiple Sequence Alignment

ClustalX - Multiple Sequence Alignment, Graphic interface

http://www.ebi.ac.uk/Tools/msa/clustalw2/

ClustalX, the graphical interface, is available in the Bioinformatics menu

ClustalW, the command line version, is available in the default PATH for all users, type clustalw2 to use

Command-line version is documented in this file, which was copied from http://helixweb.nih.gov/multi-align/man/clustalw.1.html

clustalw2 options screen ( from -options parameter )

clustalw2 help screen ( from -help parameter )

clustalw2 full help screen ( from -fullhelp parameter )

Some default parameters from clustalx for reference:

Fast-Approximate:
   Gap penalty [1-500] 5
   K-Tuple size [1-2] 2
   Top Diagonals [1-50] 4
   Window Size [1-50] 4
Slow-Accurate:
   Gap Opening [0-100] 15
   Gap Extend [0-100] 6.66
   Protein Weight Matrix Gonnet 250
   DNA Weight Matrix IUB
Multiple Alignment Parameters:
   Gap Opening [0-100] 15
   Gap Extension [0-100] 6.66
   Delay Divergence Sequences(%) 30
   DNA Transition Weight [0-1] 0.5
   Use Negative Matrix off
   Protein Weight Matrix Gonnet series
   DNA Weight Matrix IUB

Consed - A Finishing Package (BAM File Viewer, Assembly Editor, Autofinish, Autoreport, Autoedit, and Align Reads To Reference Sequence)

http://bozeman.mbt.washington.edu/consed/consed.html

consed is in the default PATH for all users. While this program has a graphical interface, I have not created a launcher in the Bioinformatics menu, because consed needs to be launched from the command line, due to required directory structure and it must be launched from within a particular directory

Consed README file, version 23.0

Consed current features

cnD - A copy number variant caller for inbred strains

http://www.sanger.ac.uk/resources/software/cnd/

The help screen from cnD

cnD README file = the manual

Installation notes

Coral - Read error corretion

http://www.cs.helsinki.fi/u/lmsalmel/coral/

Coral is an error correction algorithm for correcting reads from DNA sequencing platforms such as the Illumina Genome Analyzer or HiSeq platforms or Roche/454 Genome Sequencer

The README file included with the program

Cufflinks - Assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples

https://github.com/cole-trapnell-lab/cufflinks

Manual

The program is in the default PATH for all users

Installation notes

cutadapt - Finds and removes adapter sequences, primers, poly-A tails, etc.

https://cutadapt.readthedocs.io/en/stable/

Installation notes

DAGchainer - Computing Chains of Syntenic Genes in Complete Genomes

DAGchainer logo

http://dagchainer.sourceforge.net/

Documentation files

Installation notes

dd_detection - Find dispersed duplications in high throughput sequencing data

https://bitbucket.org/mkroon/dd_detection

README.md

Installation notes

DeconSeq - DECONtamination of SEQuence data using a modified version of BWA-SW

DeconSeq icon

http://edwards.sdsu.edu/cgi-bin/deconseq/deconseq.cgi

README

Help screen from deconseq.pl

Installation notes

Delly - Structural variant discovery by integrated paired-end and split-read analysis

https://github.com/tobiasrausch/delly

delly_parallel is in the default PATH

Installation notes

DiffSplice - Genome-Wide Detection of Differential Splicing Events with RNA-seq

http://www.netlab.uky.edu/p/bioinfo/DiffSplice

Program is installed in the default PATH for all users

Instructions are on this page

Installation notes

Dindel - Dindel: Accurate indel calls from short-read data

http://www.sanger.ac.uk/resources/software/dindel/

Dindel is a program for calling small indels from short-read sequence data ('next generation sequence data'). It is currently designed to handle only Illumina data.

Dindel takes BAM files with mapped Illumina read data and enables researchers to detect small indels and produce a VCF file of all the variant calls. It has been written in C++ and can be used on Linux-based and Mac computers (it has not been tested on Windows operating systems).

Please see the Dindel manual (Local Copy) for the full range of features.

DISCOVAR - Genome Assembler

https://software.broadinstitute.org/software/discovar/blog/

Installation notes

DISTRUCT - A program for the graphical display of population structure

http://www.stanford.edu/group/rosenberglab/distruct.html

Manual (local copy): distructManual.pdf

Publication (local copy): distructNote.pdf

Installation notes

Abstract: In analysis of multilocus genotypes from structured populations, individual coefficients of membership in subpopulations are often estimated using programs such as STRUCTURE. DISTRUCT provides a general method for visualizing these estimated membership coefficients. Subpopulations are represented as colours, and individuals are depicted as bars partitioned into coloured segments that correspond to membership coefficients in the subgroups.
 
DISTRUCT, available at www.cmb.usc.edu/~noahr/distruct.html (This link no longer works), can also be used to display subpopulation assignment probabilities when individuals are assumed to have ancestry in only one group.

EagleView - A Genome Assembly Viewer

Eagleview icon

http://www.niehs.nih.gov/research/resources/software/biostatistics/eagleview/"

The program is available to all users in the "Bioinformatics" menu

Installation notes

ea-utils -

https://github.com/zachcp/ea-utils/

Installation notes

EBSeq - An R package for identifying genes and isoforms differentially expressed (DE) across two or more biological conditions

http://www.biostat.wisc.edu/~kendzior/EBSEQ/

Commands to prepare the R environment:
library(gplots)
library(blockmodeling)
library(EBSeq)

EDirect - Entrez Direct: E-utilities on the UNIX Command Line

https://www.ncbi.nlm.nih.gov/books/NBK179288/

Installation notes

EMBOSS - A package of free, Open Source software for molecular biology

EMBOSS icon

http://emboss.sourceforge.net/

The programs are available in the default PATH for all users, so just type the name of a program to run it, e.g. needle

A list of all EMBOSS programs
"USA" Documentation

Installation notes

EST_GENOME - A program to align a spliced DNA sequence to an unspliced genomic sequence

http://www.well.ox.ac.uk/~rmott/ESTGENOME/est_genome.shtml

The two programs are available in all users' path, so just type the name of the program to run it, e.g. est_genome -help or cutout -help

The source code files for version 5.2 were dated April 27, 2004

A link to the original publication (pdf)

ESTScan - Detect coding regions in DNA/RNA sequences, even if they are of low quality

http://estscan.sourceforge.net/

Local copy of documentation user_guide_fev_07.pdf dated 2007-02-20

Installation notes

exonerate - A generic tool for sequence alignment

exonerate logo

http://www.ebi.ac.uk/~guy/exonerate/

Archive for version 2.2.0 is dated Oct 30, 2008

iPCRess : an In-silico PCR Experiment Simulation System (see the ipcress man page) is packaged with exonerate.

The exonerate package also comes with a selection of utilities for performing simple manipulations quickly on fasta files beyond 2Gb. Hopefully, their function is easy to guess from the name, but more information on their usage can be found by running them with the --help option. They are:

    esd2esi       fasta2esd        fastaannotatecdna fastachecksum fastaclean
    fastaclip     fastacomposition fastadiff         fastaexplode  fastafetch
    fastahardmask fastaindex       fastalength       fastanrdb     fastaoverlap
    fastareformat fastaremove      fastarevcomp      fastasoftmask fastasort
    fastasplit    fastasubseq      fastatranslate    fastavalidcds

Installation notes

FASTA - The FASTA program package from 1988

http://faculty.virginia.edu/wrpearson/fasta/

Manual fasta_guide.pdf (local copy)

Installation notes

fastq-tools - Small utilities for working with fastq sequence files

https://github.com/dcjones/fastq-tools

Installation notes

FastQC - A quality control application for high throughput sequence data

https://www.bioinformatics.babraham.ac.uk/projects/fastqc/

Available in the "Bioinformatics" menu on all servers

Installation notes

fastQValidator - Validates the format of fastq files

http://genome.sph.umich.edu/wiki/FastQValidator

Installation notes

fastStructure - A variational framework for inferring population structure from SNP genotype data

http://rajanil.github.io/fastStructure/

Installation notes

FASTX-Toolkit - FASTQ/A short-reads pre-processing tools

http://hannonlab.cshl.edu/fastx_toolkit/

Command-line Usage

Installation notes

fcGENE - Genotype format converter

https://sourceforge.net/projects/fcgene/

README

fcgene-1.0.7.pdf (local copy)

Installation notes

FGAP - An automated gap closing tool

http://www.bioinfo.ufpr.br/fgap/

Sourceforge page

Publication

A simpler launcher is provided. You can use the program fgap, which is in the default PATH for all users, in place of run_fgap.sh, and do not include the mcr directory parameter, it is automatically included.

Manual, obtained by running fgap without any parameters
usage.txt

Sample files can be found in /usr/local/bin/fgapdir/sample_data/

Included README file

Installation notes

FigTree - Graphical viewer of phylogenetic trees

http://tree.bio.ed.ac.uk/software/figtree/

README.txt

Example files

Installation notes

FPC - FingerPrinted Contigs

http://www.agcol.arizona.edu/software/fpc/

Available in the "Bioinformatics" menu on all servers

freebayes - Bayesian genetic variant detector

https://github.com/ekg/freebayes

Installation notes

FUNC - Analyze over- and under-representation of data associated with genes or gene products

https://func.eva.mpg.de/

The gene ontology tables have been installed to /usr/local/share/geneontology/go_201502-termdb-tables/, use this directory for the -t parameter

README file
func.html
func-refin.html

Manual pages can be accessed with man func

Installation notes

GapFiller - Closing gaps within pre-assembled scaffolds

http://www.baseclear.com/bioinformatics-tools

GapFiller v1-10 is installed in the default PATH for all users.
The program name is: GapFiller.pl

Documentation files included with the program are in /usr/local/bin/GapFiller/

Installation notes

GBrowse

http://gmod.org/wiki/Gbrowse

See also related program Topoview

Installation notes

Geometric Analysis of Structural Variants

http://compbio.cs.brown.edu/projects/gasv/

Local copy of included documentation

Installation notes

GBS-SNP-CROP - GBS SNP Calling Reference Optional Pipeline

https://github.com/halelab/GBS-SNP-CROP

Installation notes

The Genome Analysis Toolkit or The GATK - Analyse next-generation resequencing data

http://www.broadinstitute.org/gatk/index.php

A wrapper program called gatk is installed to avoid the need for the java nonsense, run GATK by typing gatk followed by appropriate parameters, for example:
gatk --help

To get the help screen for an individual program, use -T and the program name. For example:
gatk -T LiftoverVariants -h

Installation notes

gce - Genomic Character Estimator

Description, copied from the README.txt file:

GCE (genomic charactor estimator) is a bayes model based method to estimate the genome size ,genomic repeat content and the heterozygsis rate of the sequencing sample. The estimated result can be used to design the sequencing strategy.

Described in the paper Estimation of genomic characteristics by analyzing k-mer frequency in de novo genome projects Local copy

The executable gce is in the default PATH

README.txt

Howto.txt

Installation notes

Geneland - Statistical analysis of population genetics data

http://www2.imm.dtu.dk/~gigu/Geneland/

Geneland runs under R, and can be launched with a menu item under the Bioinformatics menu

Genomica - Analysis and visualization tool for genomic data

http://genomica.weizmann.ac.il/

GenomeTools - A collection of bioinformatics tools combined into a single binary named gt

http://genometools.org/

The single main program gt is available in the default PATH to all users

The help screen from gt -help

Installation notes

GFF2PS - Produces PostScript graphical output from GFF-files

http://genome.crg.es/software/gfftools/GFF2PS.html

Local copy of manual converted to pdf format MANUAL_GFF2PS_v0.96.pdf

Installation notes

GMAP - A Genomic Mapping and Alignment Program for mRNA and EST Sequences
GSNAP - Genomic Short-read Nucleotide Alignment Program

http://research-pub.gene.com/gmap/

Programs are available in the default PATH for all users

Installation notes

GNUMAP - Genomic Next-generation Universal MAPper

http://dna.cs.byu.edu/gnumap/

The command gnumap is available in the default PATH for all users

GramAlign - Time-efficient progressive Multiple Sequence Alignment

http://bioinfo.unl.edu/gramalign.php

GramAlign README

Executable is GramAlign in the default PATH

Installation notes

gridss - The genomic rearrangement identification software suite

https://github.com/PapenfussLab/gridss

Path to executable is /usr/local/bin/gridss-0.11.7-jar-with-dependencies.jar

Installation notes

gvcftools - Tools to create and analyze gVCF files

https://sites.google.com/site/gvcftools/

gvcftools usage

Installation notes

Haploview - Haplotype analysis

https://www.broadinstitute.org/scientific-community/science/programs/medical-and-population-genetics/haploview/haploview

The program is available to all users in the "Bioinformatics" menu

User Manual

Command-line operation parameters

Installation notes

Harry Plotter -

http://genomics.research.iasma.it/download.html Server no longer exists ≤1/15/2016

Readme (local copy): README.TXT

Manual (local copy): harry_plotter_doc.pdf

Installation notes

HiC-Pro - Pipeline for Hi-C processing

https://github.com/nservant/HiC-Pro

The program HiC-Pro is in the default PATH, along with the following programs:
digest_genome.py extract_snps.py hicpro2fithic.py hicpro2juicebox.sh make_viewpoints.py sparseToDense.py split_reads.py

Installation notes

HMMER - Biosequence analysis using profile hidden Markov models

http://hmmer.janelia.org/

3.1b1 Documentation (pdf)

Installation notes

HTSeq - Infrastructure to process data from high-throughput sequencing assays

http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html

http://www-huber.embl.de/users/anders/HTSeq/doc/index.html

Installation notes

iBLUP - Imputation by best linear unbiased prediction

http://klab.sjtu.edu.cn/iBLUP/ site was down Mar. 30, 2016

Scripts have been modified to be directly executable, i.e. just type iBLUP.pl to run

Installation notes

iCommands - iPlant command line tools

https://www.irods.org/index.php/icommands

Command line tools for accessing and transferring data to or from the iPlant environment

The first command to run to initialize iCommands is iinit

Installation notes

IGV - Integrative Genomics Viewer

IGV Logo

http://www.broadinstitute.org/software/igv/home

User Guide

The program is available to all users in the "Bioinformatics" menu

Installation notes

inSilicoDigestor - Restriction enzyme digestion of DNA sequence

http://comailab.genomecenter.ucdavis.edu/index.php/RESCAN

Installed to default PATH, either use full name inSilicoDigestor_multi_1.32.py or short name inSilicoDigestor

I have modified the program to increase the maximum FASTA header length reported in the output from 10 to 16 characters

There is no help screen for this program, some information copied from the source code is shown here:

# This scripts takes a reference fasta file and produces a list of cut positions for a particular restriction site,
# the length of the fragment that starts at that position (lengthF)
# and the length of the fragment that ends at that position (lengthL).
# this version adds a column with the pattern of the fragment ends

# October 2009, Luca Comai, lcomai@ucdavis.edu
# October 2010, Isabelle Henry, imhenry@ucdavis.edu
# April 2011, Luca Comai

# USAGE: inSilicoDigestor_multi_1.32.py 100 referencefile.fa catg ttaa gaattc etc
                                        ^^^ ^^^^^^^^^^^^^^^^
Documented parameters above are incorrect, they are reversed, it should be sequence file, then size cutoff!
# Where:
# reference file is a fasta file of the reference genome
# 100 (or any other number) is a cutoff for size_right: below it no site is recorded
# put at 0 if you want to record everything to file
# "catg" "ttaa" etc are the restriction site(s) of interest
# 0 index is the position at which all the enzymes cut
# 0 means before the 1st base of the restriction site
# The positions in the output file represent the first bp after the cut site

# Output:
reference           site            position            length_right    length_left
Chr1            ccccatgggg      17                      14                      14
Chr1            cttacgtaag      31                      341872          14
Chr1            gaaagctttc      341903          18270           341872
Chr1            gaaagctttc      360173          470017          18270
Chr1            gaaagctttc      830190          1093935         470017
Chr1            cttacgtaag      1924125         32993           1093935
Chr1            gaaagctttc      1957118         282019          32993

Another warning about this program, the input file must be in the current directory, i.e. no path specification, otherwise the last part fails. Copy the file or make a symlink.

InterProScan 5 - Scans a range of protein signatures against your sequence

InterProScan logo

https://github.com/ebi-pf-team/interproscan

InterProScan 5 http://code.google.com/p/interproscan/

http://code.google.com/p/interproscan/wiki/Introduction

Installation notes

Introgression Browser

https://github.com/sauloal/introgressionbrowser

Installation notes

InterProScan 4 - Scans a range of protein signatures against your sequence

http://www.geneontology.org/GO.annotation.interproscan.shtml Dead link

Binaries and data are located in /vmdata1/interproscan/iprscan/, but iprscan is available in the search path

The sample command given to test your installation is:
/vmdata1/interproscan/iprscan/bin/iprscan -cli -i /vmdata1/interproscan/iprscan/test.seq -o /vmdata1/interproscan/iprscan/test.out -format raw -goterms -iprlookup

Help screen

iTAK - Plant Transcription factor & Protein Kinase Identifier and Classifier

http://bioinfo.bti.cornell.edu/cgi-bin/itak/index.cgi

Local copy of the manual file manual.txt

To run type iTAK.pl
Important: You will have trouble if the input sequence or output directory is not in the current directory!

Output file formats are briefly summarized on the iTAK page under >>ITAK standalone program, but the tab-delimited file formats are not described.
Comparing to the web server version, the output columns are

Installation notes

JBrowse

http://jbrowse.org/

Installation notes

Jellyfish - Fast, Parallel k-mer Counting for DNA

Jellyfish logo

http://www.cbcb.umd.edu/software/jellyfish/

The newest version 2.x program jellyfish is available in the default PATH for all users, and version 1.1.11 is available as jellyfish1

Manual http://www.cbcb.umd.edu/software/jellyfish/jellyfish-manual-1.1.pdf
Local copy jellyfish-manual-1.1.pdf

Version 2 Manual

Installation notes

JoinMap3.0

Runs under Wine as a text interface program, but needs a graphic window. Avaliable in the "Bioinformatics" menu for all users.

jvarkit - Java utilities for Bioinformatics

Home page: https://github.com/lindenb/jvarkit/

List of programs available: https://github.com/lindenb/jvarkit/wiki/_pages

Installation notes

Kalign - A fast and accurate multiple sequence alignment algorithm

http://msa.sbc.su.se/cgi-bin/msa.cgi

The Kalign help screen

Installation notes

khmer - k-mer-based dataset analysis and transformations

Documentation v1.1

Installation notes

LASTZ - A tool for aligning two DNA sequences, and inferring appropriate scoring parameters automatically

https://www.bx.psu.edu/~rsharris/lastz/

Installation notes

LinkImpute, LinkImputeR - LD-kNNi algorithm, Imputation

http://www.cultivatingdiversity.org/software.html

Local copy of documentation UserGuide.pdf

Installation notes

Lumpy - General probabilistic framework for structural variant discovery

https://github.com/arq5x/lumpy-sv

Installation notes

MadMapper - Quality control, group analysis, inference of linear order

http://cgpdb.ucdavis.edu/XLinkage/MadMapper/

Suite of Python MadMapper scripts for quality control of genetic markers, group analysis and inference of linear order of markers on linkage groups.
Visualization and validation of genetic maps using two-dimensional CheckMatrix heat-plots.

I have these versions installed:
31052 Jul 30 2004 py_matrix_2D_V087_RECBIT.py
60383 Oct 29 2004 py_matrix_2D_V112_RECBIT.py
66985 Aug 11 2005 py_matrix_2D_V248_RECBIT.py ←Genetic Map 2D Matrix Plot (CheckMatrix)
154270 Aug 29 2005 Python_MadMapper_V248_RECBIT_012.py
159346 Feb 28 2008 Python_MadMapper_V248_RECBIT_016NR.py ←group analysis and quality control of genetic markers
20239 Sep 28 2005 Python_MadMapper_V248_XDELTA_016.py
29075 May 15 2007 Python_MadMapper_V248_XDELTA_119.py ←inference of linear order of markers on linkage groups using Minimum Entropy Approach and Best-Fit Extension

MAFFT - Multiple alignment program for amino acid or nucleotide sequences

http://mafft.cbrc.jp/alignment/software/

readme 7.305

Installation notes

MAKER - A portable and easily configurable genome annotation pipeline

Maker logo

http://www.yandell-lab.org/software/maker.html

Documentation

Installation notes

MAP2 - Computes a multiple global alignment of sequences using iterative pairwise method

http://deepc2.psi.iastate.edu/aat/map2/map2.html web site no longer exists Dec. 11, 2016

Documentation page

map2 is in the default PATH for all users, to use it type map2

Some information copied from the doc page

The MAP program computes a multiple global alignment of sequences using iterative pairwise method. The underlying algorithm for aligning two sequences computes a best overlapping alignment bewteen two sequences without penalizing terminal gaps. In addition, long internal gaps in short sequences are not heavily penalized. So MAP is good at producing an alignment where there are long terminal or internal gaps in some sequences. The MAP program is designed in a space-efficient manner, so long sequences can be aligned. Note that sequences must be all DNA/cDNA sequences or all protein sequences.

Program parameters (obtained by running map2 with no parameters):

Usage: /usr/local/bin/map2 Seq major_diff mismatch gap_open gap_extend

Seq           file of multiple sequences in FASTA format
major_diff    gap length for a constant gap penalty, a positive integer
mismatch      a negative integer for DNA or PAM250/BLOSUM62 for protein
gap_open      gap open penalty, a non-negative integer
gap_extend    gap extension penalty, a positive integer

Mauve - Multiple Genome Alignment

Mauve logo

http://asap.ahabs.wisc.edu/mauve/

The program is available to all users in the "Bioinformatics" menu

Local copy of README
Local copy of mauve_user_guide.pdf

Installation notes

mesquite - A modular system for evolutionary analysi

http://mesquiteproject.org/
and documentation is at http://mesquiteproject.wikispaces.com/

The program is available to all users in the "Bioinformatics" menu

Installation notes

matrix2png - Imaging all kinds of matrix-based data

http://www.chibi.ubc.ca/matrix2png/

Documentation

Installation notes

MCL - Markov Clustering algorithm

http://micans.org/mcl/

Installation notes

MCScan - Simultaneously scan multiple genomes to identify homologous chromosomal regions

http://chibba.agtec.uga.edu/duplication/mcscan/

The program executable name is mcscan and is available in the default PATH
The helper program filter_blast.py is available in the default PATH, but to avoid possible conflicts was renamed to mcscan_filter_blast.py

Documentation:

Installation notes

MCScanX and MCScanX-transposed - Multiple Collinearity Scan toolkit

MCScanX: http://chibba.pgml.uga.edu/mcscan2/

MCScanx: https://github.com/wyp1125/MCScanx

Link to the MCScanX manual http://chibba.pgml.uga.edu/mcscan2/documentation/manual.pdf

The executable in the MCScanX-transposed is a different compiled size than the one in the MCScanX directory. For this reason, nothing is installed to the default PATH, to allow selecting the correct one.
For MCScanX, use: /usr/local/bin/MCScanX/MCScanX
For MCScanX-transposed, there are several programs, use:
/usr/local/bin/MCScanX-transposed/ plus one of:
set_operation.pl, detect_tra_epochs_for_a_family.pl, detect_dup_modes_for_a_gene.pl, detect_dup_modes_for_a_family.pl, add_ka_ks.pl, MCScanX-transposed.pl, MCScanX
For MCScanx (GitHub version), use: /usr/local/bin/MCScanx/MCScanX

To use MCScanX|x downstream analysis java programs, first execute
export CLASSPATH=/usr/local/bin/MCScanX/downstream_analyses:$CLASSPATH
or export CLASSPATH=/usr/local/bin/MCScanx/downstream_analyses:$CLASSPATH
as appropriate

Installation notes

MEGA2 - Manipulation Environment for Genetic Analyses

https://watson.hgen.pitt.edu/docs/mega2_html/mega2.html

Installation notes

MEGA-CC - Molecular Evolutionary Genetics Analysis

http://www.megasoftware.net/index.php

The executable commands are megaproto (requires X session) and megacc
Output from megacc -help

Online manual

MEGA-CC Quick Start Tutorial

Installation notes

MEGAHIT - Single node assembler for large and complex metagenomics NGS reads

https://github.com/voutcn/megahit

MEGAHIT wiki

Installation notes

MELT - Mobile Element Locator Tool

http://melt.igs.umaryland.edu/index.php

Documentation

Installation notes

MEME - Motif-based sequence analysis tools

MEME logo

http://meme-suite.org/

Installation notes

MergeMap - Constructs consensus genetic maps from a set of individual maps

http://alumni.cs.ucr.edu/~yonghui/mgmap.html

Note that the executable name is consensus_map.exe, and the single parameter supplied should be the name of the configuration file (see web page for sample files).

minimap2 - A versatile pairwise aligner for genomic and spliced nucleotide sequences

https://github.com/lh3/minimap2

Access the man page with man minimap2

Installation notes

MIRA - A whole genome shotgun and EST sequence assembler for Sanger, 454, Illumina, and PacBio

http://sourceforge.net/apps/mediawiki/mira-assembler/

The program is available in the default PATH for all users

http://sourceforge.net/apps/mediawiki/mira-assembler/index.php?title=Main_Page#Documentation

Installation notes

MISA - Exact Small Sequence Repeat Detection

http://pgrc.ipk-gatersleben.de/misa/

A brief description from the

This tool allows the identification and localization of perfect microsatellites as well as compound microsatellites which are interrupted by a certain number of bases.
In order to design primers flanking the microsatellite loci, two perl scripts serve as interface modules for the program-to-program data interchange between MISA and the primer modelling software Primer3 (Whitehead Institute).

I have created a wrapper program to make running the original MISA script a bit easier, it is called bb.misa and is in the default PATH for all users

MITOFY - For plant mitochondrial genome annotation

http://dogma.ccbb.utexas.edu/mitofy/

Local copy of the manual README.pdf

A public web server implementation is available at /cgi-bin/mitofy/vcrumitofy.cgi

MochiView - Integrates browsing of genomic sequences, features, and data with DNA motif visualization and analysis

http://johnsonlab.ucsf.edu/mochi.html

The program is available to all users in the "Bioinformatics" menu

MOSAIK is a reference-guided aligner for next-generation sequencing technologies

Mosaik Assembler Logo

References

Here is an example shell script of all the steps needed to align 454 reads to a reference FASTA file, assuming you have first created FASTQ files out of the SFF files (see sff2fastq)
01.assemble.sh

MrBayes

http://mrbayes.sourceforge.net/

Manual

Installation notes

Micro-read substitution-only Fast Alignment Search Tool

http://sfu-compbio.github.io/mrsfast/

nwutils_tutorial-1.6.pdf

Installation notes

MS Mit Selektion, msms: (ms)2 - A coalescent Simulation tool with selection

https://www.mabs.at/ewing/msms/

Installation notes

MSTMap - Constructs genetic linkage maps

http://alumni.cs.ucr.edu/~yonghui/mstmap.html

Executable has been renamed to MSTMap

MUMmer - Ultra-fast alignment of large-scale DNA and protein sequences

Mummer logo

References

The programs are available in all users' path, so just type the name of a MUMmer program to run it, e.g. nucmer

I have written one supplemental program, bb.mummer which can be used to extract sequences that have a hit to a reference sequence. This program is also available to all users, type bb.mummer to see how to use it.
For example, I used it to extract all contigs with a match to chloroplast sequence using something like this:

nucmer --prefix=YourID "Referencefile.fasta" "454AssemblyFile.fna" --maxmatch
delta-filter "YourID.delta" -l 100 -u 70 -m > "FilteredID.delta"
bb.mummer --dothis=getfasta --infile="YourID.coords" --query="454AssemblyFile.fna" --outfile="hits.fasta"
nucmer --prefix=YourHitID "Referencefile.fasta" "Hits.fasta" --maxmatch
delta-filter "YourHitID.delta" -l 100 -u 70 -m > "FilteredHitsID.delta"
# You must run this next command in an X10 terminal to interactively view the plot
mummerplot.modified FilteredHitsID.delta -R "Referencefile.fasta" -Q "Hits.fasta" --layout --prefix=YourHitID

Installation notes

MUSCLE - Multiple sequence alignment Faster and more accurate than CLUSTALW

http://www.drive5.com/muscle/

The program muscle version 3.8.31 is in the default PATH for all users
Version 3.8.31b is available as muscle3.8.31b
Version 3.8.425 is available as muscle3.8.425

MUSCLE user guide as a PDF file or as a web page

Installation notes

MView - Reformats a sequence database search or a multiple alignment

http://bio-mview.sourceforge.net/index.html

On line manual

Included documentation

Installation notes

ncbi-tools - The NCBI C++ Toolkit

http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/

Installation notes

Newick Utilities - Shell tools for processing phylogenetic trees

http://cegg.unige.ch/newick_utils

nwutils_tutorial-1.6.pdf

Installation notes

novoMIR - De novo prediction of microRNA-coding regions

References

Installed to default PATH for all users, executable is novomir.pl

Oases - De novo transcriptome assembler for very short reads

References

The software is available in a directory which reflects the current version number, e.g. /usr/local/bin/oases_0.1.19/

The following information was copied from the Oases home page:

Oases is a de novo transcriptome assembler designed to produce transcripts from short read sequencing technologies, such as Illumina, SOLiD, or 454 in the absence of any genomic assembly. It was developed by Marcel Schulz (MPI for Molecular Genomics) and Daniel Zerbino (previously at the European Bioinformatics Institute (EMBL-EBI), now at UC Santa Cruz).

Oases is based on Velvet.

Installation notes

Organelle_PBA - de-novo PacBio assembly of any organelle genome

https://github.com/aubombarely/Organelle_PBA

The program name is OrganelleRef_PBA, and is available in the default PATH

Installation notes

OrthoMCL - Genome-scale Algorithm for Grouping Orthologous Protein Sequences

http://www.orthomcl.org/orthomcl/

OrthoMCL Algorithm Document

Included documentation from version 2.0.9

Installation notes version 2.0.9

Installation notes version 1.2

PAGIT - Post Assembly Genome Improvement Toolkit

https://www.sanger.ac.uk/science/tools/pagit

Because of many changes PAGIT makes to the environment, PAGIT is not installed in the default PATH.
Before use, you will need to type

source /usr/local/bin/PAGIT/sourceme.pagit
or type the following alias for the above command
pagitinit

Installation notes

PANDAseq - PAired-eND Assembler for DNA sequences

https://github.com/neufeld/pandaseq

PANDASEQ is a program to align Illumina reads, optionally with PCR primers embedded in the sequence, and reconstruct an overlapping sequence.

Documentation

paup -

https://people.sc.fsu.edu/~dswofford/paup_test/

Installation notes

PBJelly - Genome Upgrading using Long-Read Sequencing

Installed only on the PacBio virtual machine 2.0.1

http://sourceforge.net/projects/pb-jelly/

Publication: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0047768

Documentation is in the README.txt file

Installation notes

PBSIM - Pac Bio reads simulator

https://code.google.com/p/pbsim/

README

Installation notes

Pear - Paired-End reAd mergeR

http://www.exelixis-lab.org/pear

README

Installation notes

PfamScan - Search against Pfam's library of profile HMMs

Publication http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2808889/

The pfam_scan tool is a Perl wrapper around the HMMER package that allows protein sequences (in FASTA format) to be searched against Pfam’s library of profile HMMs, with the results post-processed in a similar fashion to that performed internally within Pfam.

Installation notes

PHASE - Software for haplotype reconstruction, and recombination rate estimation from population data

http://stephenslab.uchicago.edu/software.html#phase

Instructions: instruct2.1.pdf

The program, accessible in the default PATH, is PHASE

Picard - Java-based command-line utilities that manipulate SAM files

http://broadinstitute.github.io/picard/

List of programs http://broadinstitute.github.io/picard/

To run a particular program, for example to run BamIndexStats, use this syntax:
java -Xmx2g -jar /usr/local/bin/picard-tools/BamIndexStats.jar

For convenience, and if 4 gigabytes is adequate, you can use the wrapper program picard, for example
$ picard BamIndexStats INPUT=bogus.bam

Installation notes

Pilon - Automatically improve draft assemblies, find variation among strains, including large event detection

https://github.com/broadinstitute/pilon/wiki

Installation notes

Pindel - Detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants

http://gmt.genome.wustl.edu/pindel/current/

The programs bam2pindel.pl pindel pindel2vcf sam2pindel are available in the default PATH for all users

User Manual

Installation notes

PipMaker and MultiPipMaker - Compute alignments of similar regions in two DNA sequences

http://pipmaker.bx.psu.edu/pipmaker/

Installation notes

PlantTFcat - Plant Transcription Factor and Transcriptional Regulator Categorization and Analysis

http://plantgrn.noble.org/PlantTFcat/

Publication

Command line backend pipeline is called with full path /usr/local/bin/PlantTFcat/PlantTFcat.sh
Backend pipeline usage

Notes: Input FASTA must not contain blank lines, corresponding error message is
Caught: java.lang.Exception: File size error, please make sure the FASTA file is unix format (without '\r' letter) or DOS format

Installation notes

Platanus - Genome Assembler

http://platanus.bio.titech.ac.jp/

Publication in Genome Research

README file version 1.2.4 local copy (version number 1.2.3 internally)

Installation notes

PHYLIP - A free package of programs for inferring phylogenies

http://evolution.gs.washington.edu/phylip.html

Local copy of included documentation

Installation notes

plink - Whole genome association analysis toolset

http://pngu.mgh.harvard.edu/~purcell/plink/

Version 1.90 plink is available in the default PATH, the old version is also available as plink-1.07

Installation notes

Pophelper - processing output results from programs used in the analysis of population structure

http://royfrancis.github.io/pophelper/

Installation notes

Price - Paired-Read Iterative Contig Extension, a de novo genome assembler

http://derisilab.ucsf.edu/software/price/index.html

The program is installed in the default PATH, type PriceTI to run it

A local copy of the program documentation: index.html
And the readme file included with the program: README.txt

Some notes: PRICE does not support reading gzip compressed files, and it hangs if a named pipe is used. So any read files will have to be temporarily uncompressed

Installation notes

Primer3 - PCR Primer Design Program

http://primer3.sourceforge.net/

Primer3 Manual (online)
Copy of manual included with primer3

The current 2.3.6 version programs are available in the default PATH, however the older version 1.1.4 is also available for compatibility with some programs.
To select it, first use
$ export PATH="/usr/local/bin/primer3v1:$PATH"

A web interface is available at Primer3Plus

Installation notes

PRINSEQ - PRe-process and show INformation of SEQuence data

http://prinseq.sourceforge.net/

http://prinseq.sourceforge.net/manual.html#STANDALONE

The programs prinseq-lite and prinseq-graphs are available in the default PATH for all users

The PRINSEQ README file
Output from prinseq-lite -h is prinseq-lite.help.txt
Output from prinseq-graphs -h is prinseq-graphs.help.txt

Supplied example: example/example1.html

Installation notes

QMCN - Quartet MaxCut

http://research.haifa.ac.il/~ssagi/software/

Installation notes

R - A language and environment for statistical computing and graphics

http://www.r-project.org/

A launcher for R is available in the bioinformatics menu.
Type R to start R
type q() to exit R

Installation notes

RAPTR-SV - Read Pair split-read Structural Variant

https://github.com/njdbickhart/RAPTR-SV

Installation notes

RATT - Transfer annotation from a reference genome to an unannotated genome

http://ratt.sourceforge.net/

Documentation (local copy)

Installation notes

RAxML - Randomized Axelerated Maximum Likelihood

http://sco.h-its.org/exelixis/web/software/raxml/index.html

Installation notes

rclone - rsync for cloud storage

https://github.com/ncw/rclone

Installation notes

readDepth - A parallel R package for detecting copy-number alterations from short sequencing reads

https://github.com/chrisamiller/readdepth

There is a set of programs to help make annotations, createCustomAnnotations.
These programs runEachChr.sh, allSeq.pl, and mapAndGc.pl are all in the default PATH for all users.

the README file for createCustomAnnotations programs: README

Installation notes

Readseq - Read & reformat biosequences

http://iubio.bio.indiana.edu/soft/molbio/readseq/java/

Type Readseq at the command prompt to run.
Note that there is also a different program installed named readseq

This program also has a graphic interface version built in, this version is available in the "Bioinformatics" menu

REAPR - A universal tool for genome assembly evaluation

http://www.sanger.ac.uk/resources/software/reapr/

manual.pdf

README

Installation notes

RECORD - Ordering of loci on genetic linkage maps

The program RECORD (REcombination Counting and ORDering) can be used for the ordering of loci on genetic linkage maps. The method minimises the total number of recombination events. The search algorithm is a heuristic procedure, combining elements of branch-and-bound with local reshuffling.

http://www.wageningenur.nl/en/show/RECORD.htm

There is a Windows version, it can be run under WINE, it is in the "Bioinformatics" menu

There is a DOS version, it can also be run using WINE, just type ord at the command prompt

Usage:
ord [loc=name[.ext]] [log=name[.ext]] [rip=value] [eqv=value]
loc:   input  file (default ext is .loc)
log:   output file (default ext is .log)
rip:   interval for rippling
eqv:   threshold for (almost) equivalent orders
Examples:
ORD loc=tomato log=tomato rip=1 eqv=3
      (file names default to tomato.loc and tomato.log)
ORD eqv=5 rip=0 log=tom.r12 loc=tomato12.loc

RepeatExplorer - Graph-based clustering and characterization of repetitive sequences

http://repeatexplorer.umbr.cas.cz/

RepeatExplorer Manual

README.txt

Output from seqclust_cmd.py -h = seqclust_cmd.txt

Installation notes

RepeatMasker - Screen DNA sequences for interspersed repeats and low complexity DNA sequences

http://www.repeatmasker.org/

Installation notes

RNAmmer - Predicts 5s/8s, 16s/18s, and 23s/28s ribosomal RNA

http://www.cbs.dtu.dk/services/RNAmmer/

Installation notes

Rnnotator - de novo assembly of RNA-Seq data without need for a reference genome

Manual: Rnnotator2.3Manual.pdf

The program is installed in /usr/local/bin/rnnotator, this is not currently in the default PATH

Video describing Rnnotator pipeline: http://www.scivee.tv/node/19174

Description from the manual:

Comprehensive annotation and quantification of transcriptomes are outstanding problems in functional genomics. Rnnotator is an automated software pipeline that generates transcript models by de novo assembly of RNA-Seq data without the need for a reference genome. The contigs produced by Rnnotator are highly accurate and reconstruct fulllength genes when transcripts are sequenced sufficiently deep, roughly 30X for a given transcript. Rnnotator was designed to assemble Illumina single or paired-end reads. Rnnotator is also able to incorporate strand-specific RNA-Seq reads into the assembly in order to further improve the assembly.

Roche 454 software

Link to Roche instructions

See the Roche instructions page

RSEM - Estimate gene and isoform expression levels from RNA-Seq data

http://deweylab.biostat.wisc.edu/rsem/

Documentation README for RSEM

Installed in the default PATH for all users

Installation notes

Sabre - A barcode demultiplexing and trimming tool for FastQ

https://github.com/najoshi/sabre

Readme file: README.md

samblaster - A tool to mark duplicates and extract discordant and split reads from sam files

https://github.com/GregoryFaust/samblaster

Local copy of SAMBLASTER_Supplemental.pdf

Installation notes

SAMStat - Displays various properties of next-generation sequencing reads stored in SAM/BAM format

http://samstat.sourceforge.net/

README

Installation notes

SAMtools - Various utilities for manipulating alignments in the SAM and BAM formats

http://samtools.sourceforge.net/

SAMtools Wiki

SAMtools Manual

Note that the default version is 0.1.19. To run the newer 1.xx version, execute this command prior to running
export PATH="/usr/local/bin/samtools1/bin:$PATH"

The SAM Format Specification (pdf)

Installation notes for SAMtools version 0.1.19

Installation notes for SAMtools version 1.xx

Savant Genome Browser

http://www.genomesavant.com/p/savant/index

Documentation is available at http://www.genomesavant.com/p/savant/learn

The program is available to all users in the "Bioinformatics" menu

SeqGrapheR - Repeat Cluster Visualization

http://w3lamc.umbr.cas.cz/lamc/resources.php

Publication is BMC Bioinformatics 2010, 11:378

Manual SeqGrapheR_manual.pdf (local copy)

The program is available to all users in the "Bioinformatics" menu

Installation notes

SeqMonk - Mapped Sequence Analysis Tool

http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/

SeqMonk documentation http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/Help/
or the material from the SeqMonk training course http://www.bioinformatics.babraham.ac.uk/training.html#seqmonk

The program is available to all users in the "Bioinformatics" menu

You will need to configure a cache directory, and a genomes directory. I have set up "/seqmonkcache" and "/seqmonkgenomes" directories for this purpose

seqtk - Toolkit for processing sequences in FASTA/Q formats

https://github.com/lh3/seqtk

Installation notes

Sequin - NCBI's Sequence Submission Tool

http://www.ncbi.nlm.nih.gov/Sequin/index.html
Download page is http://www.ncbi.nlm.nih.gov/Sequin/download/seq_unix_download.html

This program in installed in the "Bioinformatics" menu

Documentation is at http://www.ncbi.nlm.nih.gov/Sequin/sequin.hlp.html

Installation notes

sff2fastq - Convert Roche .sff files to standard FASTQ format

This program was written by Indraniel Das, web site http://indraniel.wordpress.com/2010/04/23/sff2fastq/
This program will convert a Roche .sff format sequence file to the standard FASTQ format.

Usage: sff2fastq [options] 
        -h                  This help message
        -v                  Program and version information
        -n                  Output the untrimmed sequence and quality scores
        -o      Desired fastq output file. If not specified, defaults to stdout

For example, sff2fastq -o "/454/project/sff/FP5SLCK01.fastq" "/454/project/sff/FP5SLCK01.sff"

sff_extract - Convert paired-end sff files into paired-end fastq files

http://bioinf.comav.upv.es/sff_extract/index.html

This program will convert paired-end sff files into paired-end fastq files.
For this you will also need the linker file at /454/references/454linker.fna

SGA - String Graph Assembler

The SGA http://people.pwf.cam.ac.uk/js779/

Source code on github: https://github.com/jts/sga

The README file

Program help information sga --help

Installation notes

SHRiMP - SHort Read Mapping Package

Computational Biology Lab Logo

http://compbio.cs.toronto.edu/shrimp/

README

Here is a brief description of SHRiMP, copied from the page shown above:

SHRiMP is a software package for aligning genomic reads against a target genome. It was primarily developed with the multitudinous short reads of next generation sequencing machines in mind, as well as Applied Biosystem's colourspace genomic representation.

Documentation files in the package:

Program                 Function
-------                 --------
gmapper-cs              colourspace mapper
gmapper-ls              letterspace mapper
prettyprint-cs          pretty print alignments from rmapper/probcalc (c. space)
prettyprint-ls          pretty print alignments from rmapper/probcalc (l. space)
probcalc                parse rmapper output (non-pretty-printed output)
probcalc_mp             combine read mappings from probalc into mate pairs
shrimp_var              list detailed hit variations in rmapper/probcalc results
shrimp2sam
mergesam
fasta2fastq

Program                 Function
-------                 --------
colourise.py            convert letterspace fasta files to colourspace
extractseq.py           extract a bit of sequence from a fasta file
findseq.py              find all sequence occurrences in a fasta file
revcmpl.py              reverse-complement a contig
splitreads.py           split fasta read files into smaller chunks
splittigs.py            split fasta contig files into one file per contig

Installation notes

SignalP - Signal peptide cleavage site prediction

http://www.cbs.dtu.dk/services/SignalP/

Installation notes

SMC++ infers population history from whole-genome sequence data

https://github.com/popgenmethods/smcpp

Installation notes

SMRT Analysis - Pac Bio software

Installation notes for virtual machine, version 2.0.1

Installation notes for virtual machine, version 2.2

Installation notes for SMRT Link

Standalone version of Blasr

SNAP - Semi-HMM-based Nucleic Acid Parser

http://korflab.ucdavis.edu/software.html

00README

Installation notes

SNPhylo - A pipeline to generate a phylogenetic tree from huge SNP data

http://chibba.pgml.uga.edu/snphylo/

The program snphylo.sh is in the default PATH for all users

Program parameters in a more convenient format

   -v VCF file | -H HapMap file | -S Simple SNP file | -d GDS file
   -p Maximum percent low coverage sample (5)
   -c Minimum depth of coverage (5)
   -p Maximum percent no SNP information (5)
   -l LD_threshold (0.1)
   -m Minor Allele Frequency threshold (0.1)
   -M Missing rate (0.1)
   -o Outgroup sample name
   -P Prefix of output files (snphylo.output)
   -b (flag) enable bootstrap analysis
   -B number of bootstrap samples (100)
   -a number of the last autosome (22)
   -r (flag) skip removing low quality data
   -A (flag) perform Muscle analysis
   -h | -? (flag) print help screen

Installation notes

SNP-o-matic - A fast, memory-efficient, and stringent read mapping tool

http://snpomatic.sourceforge.net/

The program findknownsnps is in the default PATH for all users

Link to manual (PDF)

Manual included with program Manual.doc

Installation notes

SOAP - Short Oligonucleotide Analysis Package (Assembly, read mapping, etc.)

SOAP logo

http://soap.genomics.org.cn/

Documentation for "SOAPaligner/soap2" is a man page, type man soap to access it

Documentation included with "Correction tool for SOAPdenovo":
readme
correction_tool_readme.doc

Documentation included with "SOAPsplice":
readme.txt
document
example.sh
exampleGenome.fa
exampleRNA.fa

Help screen from "soap.coverage":
soap.coverage.txt

Installation notes for SOAPdenovo

MANUAL for SOAPdenovo

All help screens for SOAPdenovo2-63mer

Installation notes for SOAPec

ReadMe file for SOAPec

Installation notes for SOAPsnp

readme file for SOAPsnp

Installation notes for SOAPindel

readme file for SOAPindel

Installation notes for GapCloser

GapCloser_Manual.pdf

Spidey - mRNA to genomic alignment

Spidey banner

http://www.ncbi.nlm.nih.gov/spidey/
This web site also provides a browser interface for Spidey

Spidey documentation: http://www.ncbi.nlm.nih.gov/spidey/spideydoc.html

The program bb.spidey2image can be used to make images from command line runs of Spidey

Splicegrapher - Splice graphs of alternate splicing patterns

http://splicegrapher.sourceforge.net/

Installation notes

SplitsTree4 - Compute unrooted phylogenetic networks from molecular sequence data

http://www.phylogenetic-networks.org/

Manual

Installation notes

sprai - single pass read accuracy improver

http://zombie.cb.k.u-tokyo.ac.jp/sprai/index.html

Installation notes

sra Toolkit - Short Read Archive Toolkit from NCBI

Software page at NCBI: http://www.ncbi.nlm.nih.gov/Traces/sra/?view=software

Toolkit Documentation

Programs have been installed in the default PATH for all users, just type the name to use it, e.g.fastq-dump

Installation notes

SSPACE - Scaffolding pre-assembled contigs using NGS paired-read data

SSPACE logo

http://www.baseclear.com/bioinformatics-tools

SSPACE standard v3.0 is installed in the default PATH for all users.
The program name is: SSPACE_Standard_v3.0.pl
The program name is: SSPACE-LongRead.pl

Documentation files included with the program are in /usr/local/bin/SSPACE/

Installation notes

SSAHA2 - Sequence Search and Alignment by Hashing Algorithm

http://www.sanger.ac.uk/resources/software/ssaha2/

Manual (version 2.5.3, newest as of Aug. 2014, local copy): ssaha2man_v2.5.3.pdf

Readme file: README

Installation notes

Stacks - A software pipeline for building loci out of a set of short-read sequenced samples

Stacks logo

http://creskolab.uoregon.edu/stacks/

Documentation:

Installation notes

STAR - Aligns RNA-seq reads to a reference genome using uncompressed suffix arrays

https://github.com/alexdobin/STAR/releases

The exectuable is STAR which is available in the default PATH for all users

The manual pdf STARmanual.pdf
Local copy STARmanual.pdf

Installation notes

Structure - Investigate population structure with multi-locus genotype data

http://pritch.bsd.uchicago.edu/structure.html

The program is available to all users in the "Bioinformatics" menu

The structure documentation is available at http://pritch.bsd.uchicago.edu/structure_software/release_versions/
Local copy of documentation, version 2.3.4: structure_doc.pdf

An overview of STRUCTURE: applications, parameter settings, and supporting software

See also DISTRUCT
and CLUMPP

Installation notes

Structure Harvester - A website and program for visualizing STRUCTURE output

The web interface is at http://taylor0.biology.ucla.edu/structureHarvester/

The Python script has been installed locally, available in the default PATH: structureHarvester.py

The README file: README.md

The structureHarvester.py help screen

Installation notes

subread - A superfast read aligner

http://subread.sourceforge.net/

Manual included with the program: UserManual.pdf

Programs are installed in the default PATH for all users: remove-duplicate-reads snp-calling subjunc subread-align subread-buildindex subread-fullscan

Installation notes

SyMAP - Synteny Mapping and Analysis Program

http://www.agcol.arizona.edu/software/symap/

The program is available to all users in the "Bioinformatics" menu

Installation notes

Tablet - Next Generation Sequence Assembly Visualization

http://bioinf.scri.ac.uk/tablet/

The program is available to all users in the "Bioinformatics" menu

Installation notes

TASSEL - Trait Analysis by aSSociation, Evolution, and Linkage

https://www.maizegenetics.net/tassel

The program is available to all users in the "Bioinformatics" menu

Tassel4 standalone and Tassel5 standalone is in the default PATH for all users
Currently 4 has priority, to specify version 5 explicitly, include
PATH="/usr/local/bin/tassel-5-standalone:$PATH"
in your script

An undocumented change to TASSEL4 standalone (Tassel Version: 4.3.7 Date: April 17, 2014), the plugin TagsToSNPByAlignmentPlugin is now called DiscoverySNPCallerPlugin
I saved some helpful output from this new plugin as DiscoverySNPCallerPlugin.txt

From Tassel4-standalone: TasselPipelineCLI.pdf

Tassel 5 command line documentation

Installation notes

SVDetect - Detect genomic structural variations from paired-end and mate-pair sequencing data

http://svdetect.sourceforge.net/Site/Home.html

README file (local copy)

Manual (SVDetect web site)

The programs SVDetect and BAM_preprocessingPairs.pl are available in the default PATH for all users

Installation notes

svdetection

http://sourceforge.net/projects/svdetection

The programs PE.pl Preprocess_rm0to22.pl Preprocess_rm_normal.pl links.pl are available in the default PATH for all users

README file from sourceforge page

Installation notes

SVMerge - Enhanced structural variant and breakpoint detection

http://svmerge.sourceforge.net/

Manual SVMerge_Documentation.pdf

Installation notes

tbl2asn - NCBI Submission Tool

http://www.ncbi.nlm.nih.gov/genbank/tbl2asn2

Example .tbl files

To get the installed version number type tbl2asn - or tbl2asn --help

Installation notes

telomerecat - Telomere Computational Analysis Tool

https://github.com/jhrf/telomerecat

Installation notes

TGICL - Gene Index Clustering Tool

TGICL logo

http://compbio.dfci.harvard.edu/tgi/software/
Software download page is http://sourceforge.net/projects/tgicl/

For documentation type perldoc -F /usr/local/bin/TGICL-2.1/bin/tgicl

Description copied from the above command:

The Gene Index Clustering Tool (TGICL) is a software package that tries to efficiently cluster and create assemblies (contigs) from a set of input DNA sequences given in a fasta file. The "clustering" phase is intended to partition the input data set into smaller groups of sequences (clusters) that due to stringent similarity have a greater probability to originate from the same longer sequence. However, the clustering phase does not perform any multiple alignment but only fast pairwise alignments (using megablast), which are then filtered and used to build subsets of sequences by a transitive closure approach. In the assembly phase each such cluster is sent to the assembly program (cap3) which attempts the multiple alignment of the sequences in the cluster and creates one or more contigs (consensus sequences). Both clustering and assembly phases can be executed in parallel on multiple CPU machines or in a PVM environment.

TICR - Parallelized concordance analyses

https://github.com/nstenz/TICR

Installation notes

tmhmm - Prediction of transmembrane helices in proteins

http://www.cbs.dtu.dk/services/TMHMM/

Local copy of html file included with the program: TMHMM2.0.html

tmhmm command line parameters are not documented in this file, nor by the program!
Reconstructed documentation from the Perl source code:
--workdir=s # Working dir.
--wwwdir=s # The place where the www server looks for files (The www name for the working dir)
--serverhome=s #[not described]
--html # Produce HTML output
--short # Short output format
--plot # Produce graphics
--v1 # Use old model (version 1)
--basedir=s # basis directory for TMHMM package
--bindir=s # Bin directory (defaults basedir/bin)
--scrdir=s # Script directory (defaults basedir/bin)
--libdir=s # Library directory (defaults basedir/lib)
--d # DEBUGGING
# Give ONE fasta file on cmdline OR use stdin
# A single sequence can be given WITHOUT the ID line (">ID")
# Such a sequence will be called "WEBSEQUENCE"

Installation notes

TreeGraph - Generating complex PostScript and SVG trees using an extensible tree description format

http://www.jmüller.name/treegraph/

Local copy of documentation docu.pdf

Local copy of sample files

Installation notes

TreeGraph 2 - A graphical editor for phylogenetic trees

http://treegraph.bioinfweb.info/

TreeGraph 2 help system

Installation notes

TreeLD - Tool for mapping complex trait loci

http://pritch.bsd.uchicago.edu/software.html

Documentation http://pritch.bsd.uchicago.edu/treeld/TreeLD_Doc/Documentation.html

Publication (local copy): Bioinformatics-2005-Zollner-3168-70.pdf

TreeLD is a software tool for mapping complex trait loci, developed by Zollner and Pritchard (2005). TreeLD performs a multipoint LD-analysis by inferring the ancestry of a genomic region and analyzing this ancestry for signals of disease mutations. The generated likelihoods can be used to test for the presence of a disease locus and to fine-map its location, providing a point estimate and a credible region. Furthermore, the package provides a novel way of visualizing the association signal in a sample. TreeLD is designed for high-density SNP haplotypes and can be applied to case-control data, TDT trio data and quantitative trait data. Download TreeLD 1.0

svtyper - Bayesian genotyper for structural variants

https://github.com/hall-lab/svtyper

Installation notes

tabix - TAB-delimited file IndeXer

https://github.com/samtools/tabix

Installation notes

TIGRA - Targeted local assembly of structural variant breakpoints

TIGRA-SV version 0.1 http://gmt.genome.wustl.edu/tigra-sv/0.1/index.html ← 404 error, No longer works

TIGRA version 0.3.7 http://bioinformatics.mdanderson.org/main/TIGRA

A thread mentioning that TIGRA-SV is no longer being developed

The old version is available as tigra-sv-0.1 in the default PATH
The new version is available as tigra-sv in the default PATH

Installation notes for TIGRA-SV 0.1

Installation notes for TIGRA 0.3.7

TopHat - A fast splice junction mapper for RNA-Seq reads

http://ccb.jhu.edu/software/tophat

The program is in the default PATH for all users

Installation notes

TopoView - Track for RNAseq data in GBrowse

http://flybase.org/static_pages/docs/software/topoview.html

Installation notes

TransDecoder - Find Coding Regions Within Transcripts

http://transdecoder.github.io/

Installation notes

treemix - Inference of population trees with admixture

https://bitbucket.org/nygcresearch/treemix/wiki/Home

Documentation treemix_manual_2_14_12.pdf

Trimmomatic - A flexible read trimming tool for Illumina NGS data

http://www.usadellab.org/cms/index.php?page=trimmomatic

A wrapper for the java program is trimmomatic, available in the default PATH for all users.
Pass as the first parameter either PE or SE.
The remaining parameters are as documented on the home page

Installation notes

Trinity - RNA-Seq De novo Assembly

Trinity logo

https://github.com/trinityrnaseq/trinityrnaseq/wiki

The programs are not in the default PATH, find them at the version-independent symbolic link /usr/local/bin/trinityrnaseq/, and in subdirectories in that location.

Installation notes

Trinotate - Transcriptome Functional Annotation and Analysis

https://trinotate.github.io/

The programs are not in the default PATH, find them at the version-independent symbolic link /usr/local/bin/trinotate/, and in subdirectories in that location.

Installation notes

tRNAscan-SE - Search for tRNA genes in genomic sequence

http://lowelab.ucsc.edu/tRNAscan-SE/

man page: man tRNAscan-SE

Online manual: http://lowelab.ucsc.edu/tRNAscan-SE/Manual/Manual.html

Installation notes

UGENE - Free open-source cross-platform bioinformatics software

UGENE logo

http://ugene.unipro.ru/

Available in "Bioinformatics" menu

USEARCH - A unique high-throughput sequence analysis tool

http://drive5.com/usearch/

Installed to default PATH for all users, type usearch

USEARCH is a unique high-throughput sequence analysis tool. It is a distributed as single binary program that implements a suite of algorithms comparable to BLASTN, BLASTP, BLASTX, BLASTCLUST, CD-HIT, CD-HIT-EST, CD-HIT-2D, CD-HIT-EST-2D, CD-HIT-OTU, CD-HIT-454, ChimeraSlayer, Perseus, RAPsearch and more. It supports a rich set of sequence matching options, including E-values, identity, coverage (fraction of query or target sequence covered by the alignment) and maximum gap length, and a range of output file formats including FASTA, BLAST-like, user-defined tabbed text and a native format designed for clustering applications. Supported alignment styles include local (gapped and ungapped), like BLAST, and global, which is most often used in clustering applications. User-settable parameters allow tuning of substitution scores, gap penalties and Karlin-Altschul statistics.

VCF2Dis - p-distance matrix based Variant Call Format

https://github.com/BGI-shenzhen/VCF2Dis

Installation notes

VCFtools - Methods for working with VCF files

https://vcftools.github.io/index.html

Documentation https://vcftools.github.io/examples.html

Citation: The Variant Call Format and VCFtools, Petr Danecek, Adam Auton, Goncalo Abecasis, Cornelis A. Albers, Eric Banks, Mark A. DePristo, Robert Handsaker, Gerton Lunter, Gabor Marth, Stephen T. Sherry, Gilean McVean, Richard Durbin and 1000 Genomes Project Analysis Group, Bioinformatics, 2011
http://dx.doi.org/10.1093/bioinformatics/btr330

"bcftools/htslib VCF commands" has been installed, which is different than the samtools bcftools program, so for this version, use bcftools2.

Installation notes

Velvet - Sequence assembler for very short reads

http://www.ebi.ac.uk/~zerbino/velvet/

Velvet Manual and extension for Columbus in pdf format.

The software is available in a directory which reflects the current version number, e.g. /usr/local/bin/velvet_1.0.19/

For transcriptomic assembly Velvet is extended by Oases.

Installation notes

vg - Tools for working with variation graphs

https://github.com/vgteam/vg

Wiki

Installation notes

VSEARCH - Open source alternative to USEARCH

https://github.com/torognes/vsearch

Manual

README.md

Installation notes

WebLogo - Generate sequence logos

WebLogo logo

http://weblogo.berkeley.edu/

Installation notes

wgsim - Sequence assembler for very short reads

https://github.com/lh3/wgsim

README

Installation notes

wQMC - Phylogenic tree using the Weighted Quartet MaxCut Algorithm

http://research.haifa.ac.il/~ssagi/software/

ReadME.pdf

 12,802 Sep 29  2013 example_input_file_for_wQMC_20_leaves.txt
 49,958 Sep 29  2013 example_input_file_for_QMC_20_leaves.txt
     89 Sep 29  2013 example_output_file_of_wQMC_or_QMC.dat

XPCLR - Allele frequency differentiation at linked loci to detect selective sweeps

http://research.haifa.ac.il/~ssagi/software/

README

Installation notes

Zorro - The Masked Assembler

http://www.lge.ibi.unicamp.br/zorro/

The two programs are split_at_Ns.pl and zorro.pl, available in the default PATH

README

DOC

Installation notes