 |
 |
 |
This page was last updated on Thursday, 30-Mar-2023 12:00:57 CDT
= installed on cucumber server
= installed on cranberry server
= installed on carrot server
= installed on vaccinium server
= installed on daucus server
= installed on pickle server
ABySS-Explorer - Novel graph-based representation of sequence assembly
AliView - Lightweight alignment viewer and editor
Bambino - A graphical viewer and variant detector for NGS files in SAM/BAM format
BAMseek - A Large File Viewer for BAM and SAM alignment files
Bandage - a Bioinformatics Application for Navigating De novo Assembly Graphs Easily
BAPS - Bayesian Analysis of Population Structure
Blast2GO - Functional Annotation
ClustalX - Multiple sequence alignment
EagleView - A Genome Assembly Viewer
FastQC - A quality control application for high throughput sequence data
FPC - FingerPrinted Contigs
FigTree - Graphical viewer of phylogenetic trees
IGV - Integrative Genomics Viewer
Geneland - Statistical analysis of population genetics data
Genomica - Analysis and visualization tool for genomic data
JoinMap3.0
Haploview - Haplotype analysis
Introgression Browser
Mauve - Multiple Genome Alignment
Mesquite - A modular system for evolutionary analysis
MochiView - Integrates browsing of genomic sequences, features, and data with DNA motif visualization and analysis
Roche 454 software
Savant Genome Browser
SeqGrapheR - Repeat Cluster Visualization
SeqMonk - Mapped Sequence Analysis Tool
Sequin - NCBI's Sequence Submission Tool
Structure - Investigate population structure with multi-locus genotype data
Structure Harvester - A website and program for visualizing STRUCTURE output
SyMAP - Synteny Mapping and Analysis Program
Tablet - Next Generation Sequence Assembly Visualization
TASSEL - Trait Analysis by aSSociation, Evolution, and Linkage
TreeGraph - Generating complex PostScript and SVG trees using an extensible tree description format
TreeGraph 2 - A graphical editor for phylogenetic trees
TreeLD - Tool for mapping complex trait loci
UGENE - Free open-source cross-platform bioinformatics software
Consed - A Finishing Package
BioMart - Unified access to distributed research data
web BLAST
GBrowse
JBrowse
MITOFY - For plant mitochondrial genome annotation
PipMaker and MultiPipMaker - Computes alignments of similar regions in two DNA sequences
TopoView - Track for RNAseq data in GBrowse
ABySS - A parallel assembler for short read sequence data
Trans-ABySS - Analyze ABySS multi-k-assembled shotgun transcriptome data
admixture - Fast ancestry estimation
ALLMAPS - JCVI utility libraries
alpha-CENTAURI - Mine alpha satellites and their higher-order structures in sequence data
AMOS - A Modular, Open-Source whole genome assembler
Annovar - Functionally annotate genetic variants
Artemis - DNA sequence viewer and annotation tool
ASCIIGenome - Text only genome viewer
ASTRAL - Estimate an unrooted species tree
Augustus - A program that predicts genes in eukaryotic genomic sequences
bam-readcount - Count DNA sequence reads in BAM files
bamtools - C++ API & command-line toolkit for working with BAM data
Black Box programs - Programs Doug has written
BBMap - Short read aligner, and other bioinformatic tools
Beagle - Genotype calling, genotype phasing, imputation of ungenotyped markers, and identity-by-descent segment detection
BEAGLE (beagle-lib) - General purpose library for evaluating the likelihood of sequence evolution on trees
BEAST - Bayesian Evolutionary Analysis Sampling Trees
BEDOPS - the fast, highly scalable and easily-parallelizable genome analysis toolkit
BEDTools - A flexible suite of utilities for comparing genomic features
BFAST - Blat-like Fast Accurate Search Tool
Bioconductor - Analysis and comprehension of high-throughput genomic data with R
Biopieces - Biopieces is a bioinformatic framework of tools easily used and easily created
BLASR - Basic Local Alignment with Successive Refinement
blast (legacy version) - Basic Local Alignment Search Tool
BLAST+ - Basic Local Alignment Search Tool
Blat - Fast alignment of similar sequences
blobology - Blobplots or Taxon-Annotated-GC-Coverage plots (TAGC plots)
Bowtie and Bowtie 2 - An ultrafast memory-efficient short read aligner
Breakdancer - genome-wide detection of structural variants from paired-end reads
BSMAPz - short reads mapping program for bisulfite sequencing in DNA methylation study
BUCKy - A Program for Bayesian Concordance Analysis
BUSCO - Assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs
BWA - Burrows-Wheeler Aligner
canu - A single molecule sequence assembler for genomes large and small
CAP3 - Sequence Assembly Program
CarthaGène - A genetic/radiated hybrid mapping software
Celera Assembler - A de novo whole-genome shotgun (WGS) DNA sequence assembler
CD-HIT - program for clustering DNA/protein sequence database at high identity with tolerance
cdbfasta / cdbyank - Fasta file indexing and retrival tool
Circos - Circular Visualization
CLUMPP - Label switching and multimodality problems in population-genetic cluster analyses
ClustalW2 - Multiple Sequence Alignment
Clustal Omega - Multiple Sequence Alignment
cnD - A copy number variant caller for inbred strains
Coral - Read error correction
Cufflinks - Assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples
cutadapt - Finds and removes adapter sequences, primers, poly-A tails, etc.
DAGchainer - Computing Chains of Syntenic Genes in Complete Genomes
dd_detection - Find dispersed duplications in high throughput sequencing data
DeconSeq - DECONtamination of SEQuence data using a modified version of BWA-SW
Delly - Structural variant discovery by integrated paired-end and split-read analysis
DiffSplice - Genome-Wide Detection of Differential Splicing Events with RNA-seq
Dindel - Accurate indel calls from short-read data
DISCOVAR - Genome Assembler
DISTRUCT - A program for the graphical display of population structure
ea-utils -
EBSeq - An R package for identifying genes and isoforms differentially expressed (DE) across two or more biological conditions
EDirect - Entrez Direct: E-utilities on the UNIX Command Line
EMBOSS - A package of free, Open Source software for molecular biology
EST_GENOME - Align a spliced DNA sequence to an unspliced genomic sequence
ESTScan - Detect coding regions in DNA/RNA sequences, even if they are of low quality
exonerate - A generic tool for sequence alignment
FASTA - The FASTA program package from 1988
fastp - A tool designed to provide fast all-in-one preprocessing for FastQ files
fastsimcoal2 - fast sequential Markov coalescent simulation of genomic data under complex evolutionary models
fastStructure - A variational framework for inferring population structure from SNP genotype data
fastq-tools - Small utilities for working with fastq sequence files
fastQValidator - Validates the format of fastq files
FASTX-Toolkit - FASTQ/A short-reads pre-processing tools
fcGENE - Genotype format converter
FGAP - An automated gap closing tool
freebayes - Bayesian genetic variant detector
FUNC - Analyze over- and under-representation of data associated with genes or gene products
GapFiller - Closing gaps within pre-assembled scaffolds
gasv - Geometric Analysis of Structural Variants
GBS-SNP-CROP - GBS SNP Calling Reference Optional Pipeline
The Genome Analysis Toolkit or GATK - Analyse next generation sequencing data
gigabayes
gce - Genomic Character Estimator
GenomeTools - A collection of bioinformatics tools combined into a single binary named gt
GFF2PS - Produces PostScript graphical output from GFF-files
GMAP and GSNAP - Read Mapping and Alignment
gnumap - Genomic Next-generation Universal MAPper
GramAlign - Time-efficient progressive Multiple Sequence Alignment
gridss - The genomic rearrangement identification software suite
gvcftools - Tools to create and analyze gVCF files
Harry Plotter -
HiC-Pro - Pipeline for Hi-C processing
HMMER - Biosequence analysis using profile hidden Markov models
HTSeq - Infrastructure to process data from high-throughput sequencing assays
iBLUP - Imputation by best linear unbiased prediction
iCommands - iPlant command line tools
inSilicoDigestor - Restriction enzyme digestion of DNA sequence
iTAK - Plant Transcription factor & Protein Kinase Identifier and Classifier
InterProScan 5 - Scans a range of protein signatures against your sequence
InterProScan 4 - Scans a range of protein signatures against your sequence
Jellyfish - Fast, Parallel k-mer Counting for DNA
jvarkit - Java utilities for Bioinformatics
Kalign - A fast and accurate multiple sequence alignment algorithm
khmer - k-mer-based dataset analysis and transformations
LASTZ - A tool for aligning two DNA sequences, and inferring appropriate scoring parameters automatically
LinkImpute, LinkImputeR - LD-kNNi algorithm, Imputation
Lumpy - General probabilistic framework for structural variant discovery
MadMapper - Quality control, group analysis, inference of linear order
MAFFT - Multiple alignment program for amino acid or nucleotide sequences
MAKER - A portable and easily configurable genome annotation pipeline
MAP2 - Computes a multiple global alignment of sequences using iterative pairwise method
matrix2png - Imaging all kinds of matrix-based data
MCL - Markov Clustering algorithm
MEGA2 - Manipulation Environment for Genetic Analyses
MEGA-CC - Molecular Evolutionary Genetics Analysis
MEGAHIT - Single node assembler for large and complex metagenomics NGS reads
MELT - Mobile Element Locator Tool
MEME - Motif-based sequence analysis tools
MergeMap - Constructs consensus genetic maps from a set of individual maps
MCScan - Simultaneously scan multiple genomes to identify homologous chromosomal regions
MCScanX and MCScanX-transposed - Multiple Collinearity Scan toolkit
minimap2 - A versatile pairwise aligner for genomic and spliced nucleotide sequences
MIRA - A whole genome shotgun and EST sequence assembler for Sanger, 454, Illumina, and PacBio
MISA - Exact Small Sequence Repeat Detection
MOSAIK - A reference-guided aligner for next-generation sequencing technologies
MrBayes - Bayesian Inference of Phylogeny
mrsFAST - Micro-read substitution-only Fast Alignment Search Tool
MS Mit Selektion, msms: (ms)2 - A coalescent Simulation tool with selection
MSTMap - Constructs genetic linkage maps
MUMmer - Ultra-fast alignment of large-scale DNA and protein sequences
MUSCLE - Multiple sequence alignment Faster and more accurate than CLUSTALW
MView - Reformats a sequence database search or a multiple alignment
ncbi-tools - The NCBI C++ Toolkit
Newick Utilities - Shell tools for processing phylogenetic trees
novoMIR - De novo prediction of microRNA-coding regions
Oases - De novo transcriptome assembler for very short reads
Organelle_PBA - de-novo PacBio assembly of any organelle genome
OrthoMCL - Genome-scale Algorithm for Grouping Orthologous Protein Sequences
PAGIT - Post Assembly Genome Improvement Toolkit
PANDASEQ - PAired-eND Assembler for DNA sequences
paup -
PBJelly - Genome Upgrading using Long-Read Sequencing
PBSIM - Pac Bio reads simulator
Pear - Paired-End reAd mergeR
PfamScan - Search against Pfam's library of profile HMMs
PHASE - Software for haplotype reconstruction, and recombination rate estimation from population data
Picard - Java-based command-line utilities that manipulate SAM files
Pilon - Automatically improve draft assemblies, find variation among strains, including large event detection
Pindel - Detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants
Platypus - A Haplotype-Based Variant Caller For Next Generation Sequence Data
PlantTFcat - Plant Transcription Factor and Transcriptional Regulator Categorization and Analysis
Platanus - Genome Assembler
PHYLIP - A free package of programs for inferring phylogenies
plink - Whole genome association analysis toolset
Pophelper - processing output results from programs used in the analysis of population structure
Price - Paired-Read Iterative Contig Extension, a de novo genome assembler
Primer3 - PCR Primer Design
PRINSEQ - PRe-process and show INformation of SEQuence data
QMCN - Quartet MaxCut
R - A language and environment for statistical computing and graphics
RAPTR-SV - Read Pair split-read Structural Variant
RATT - Transfer annotation from a reference genome to an unannotated genome
RAxML - Randomized Axelerated Maximum Likelihood
rclone - rsync for cloud storage
readDepth - A parallel R package for detecting copy-number alterations from short sequencing reads
Readseq - Read & reformat biosequences
REAPR - A universal tool for genome assembly evaluation
RECORD - Ordering of loci on genetic linkage maps
RepeatExplorer - Graph-based clustering and characterization of repetitive sequences
RepeatMasker - Screen DNA sequences for interspersed repeats and low complexity DNA sequences
RNAmmer - Predicts 5s/8s, 16s/18s, and 23s/28s ribosomal RNA
Rnnotator - de novo assembly of RNA-Seq data without need for a reference genome
RSEM - Estimate gene and isoform expression levels from RNA-Seq data
Sabre - A barcode demultiplexing and trimming tool for FastQ
samblaster - A tool to mark duplicates and extract discordant and split reads from sam files
SAMStat - Displays various properties of next-generation sequencing reads stored in SAM/BAM format
SAMtools - Various utilities for manipulating alignments in the SAM and BAM formats
seqtk - Toolkit for processing sequences in FASTA/Q formats
sff2fastq - Convert Roche .sff files to standard FASTQ format
sff_extract - Convert paired-end sff files into paired-end fastq files
SGA - String Graph Assembler
SHRiMP - SHort Read Mapping Package
signalp - Signal peptide cleavage site prediction
SMC++ - infers population history from whole-genome sequence data
SMRT Analysis - Pac Bio Software
SNAP - Semi-HMM-based Nucleic Acid Parser
SNPhylo - A pipeline to generate a phylogenetic tree from huge SNP data
SNP-o-matic - A fast, memory-efficient, and stringent read mapping tool
SOAP - Short Oligonucleotide Analysis Package (Assembly, read mapping, etc.)
Spidey - mRNA to genomic alignment
SpliceGrapher - Splice graphs of alternate splicing patterns
SplitsTree4 - Compute unrooted phylogenetic networks from molecular sequence data
sprai - single pass read accuracy improver
sra Toolkit - Short Read Archive Toolkit from NCBI
SSAHA2 - Sequence Search and Alignment by Hashing Algorithm
SSPACE - Scaffolding pre-assembled contigs using NGS paired-read data
Stacks - A software pipeline for building loci out of a set of short-read sequenced samples
STAR - Aligns RNA-seq reads to a reference genome using uncompressed suffix arrays
subread - A superfast read aligner
SVDetect - Detect genomic structural variations from paired-end and mate-pair sequencing data
svdetection
SVMerge - Enhanced structural variant and breakpoint detection
svtyper - Bayesian genotyper for structural variants
tabix - TAB-delimited file IndeXer
tbl2asn - NCBI Submission Tool
telomerecat - Telomere Computational Analysis Tool
TGICL - Gene Index Clustering Tool
TIGRA - Targeted local assembly of structural variant breakpoints
TICR - Parallelized concordance analyses
tmhmm - Prediction of transmembrane helices in proteins
TopHat - A fast splice junction mapper for RNA-Seq reads
TransDecoder - Find Coding Regions Within Transcripts
treemix - Inference of population trees with admixture
Trimmomatic - A flexible read trimming tool for Illumina NGS data
Trinity - RNA-Seq De novo Assembly
Trinotate - Transcriptome Functional Annotation and Analysis
tRNAscan-SE - Search for tRNA genes in genomic sequence
USEARCH - A unique high-throughput sequence analysis tool
VCF2Dis - p-distance matrix based Variant Call Format
VCFtools - Methods for working with VCF files
Velvet - Sequence assembler for very short reads
vg - Tools for working with variation graphs
VSEARCH - Open source alternative to USEARCH
WebLogo - Generate sequence logos
wgsum - Tool for simulating sequence reads from a reference genome
wQMC - Phylogenic tree using the Weighted Quartet MaxCut Algorithm
XPCLR - Allele frequency differentiation at linked loci to detect selective sweeps
Zorro - The Masked Assembler
http://www.bcgsc.ca/platform/bioinfo/software/abyss
Original Publication
Other Publications using ABySS
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
http://www.bcgsc.ca/platform/bioinfo/software/trans-abyss
http://www.ormbunkar.se/aliview/
A local copy of the manual: admixture-manual.pdf
http://www.ormbunkar.se/aliview/
https://github.com/tanghaibao/jcvi/wiki/ALLMAPS
https://github.com/volkansevim/alpha-CENTAURI
http://sourceforge.net/apps/mediawiki/amos/
BAMBUS2 is part of AMOS
http://annovar.openbioinformatics.org/
http://www.sanger.ac.uk/science/tools/artemis
https://github.com/dariober/ASCIIGenome
https://github.com/smirarab/ASTRAL
http://bioinf.uni-greifswald.de/augustus/
Augustus config directory is set to
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
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
https://github.com/pezmaster31/bamtools
https://github.com/pezmaster31/bamtools
Using the toolkit (pdf)
http://rrwick.github.io/Bandage/
http://web.abo.fi/fak/mnf/mate/jc/software/baps.html
The program is available to all users in the "Bioinformatics" menu
https://github.com/dsenalik/bb
Type
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)
Here is a local copy of the included
http://faculty.washington.edu/browning/beagle/beagle.html
A wrapper program
Beagle version 5.2 documentation
(Local copy)
https://github.com/beagle-dev/beagle-lib
https://github.com/beast-dev/beast-mcmc
https://bedops.readthedocs.org/en/latest/
https://github.com/arq5x/bedtools2
The command-line programs are available in the default PATH for all users
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
Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language
The base Bioconductor packages are installed and available in the R environment
http://maasha.github.io/biopieces/
To use, you will have to
# 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
http://bix.ucsd.edu/projects/blasr/
BLASR help output from
BLASR help output from
The program is available to all users in the "Bioinformatics" menu
Obsolete: 
Installation notes for local Blast2GO database installation
http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download
http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download
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
https://github.com/blaxterlab/blobology
Bowtie 1 is available in the default PATH for all users on all computers
Bowtie 2 is available in the default PATH for all users on all computers
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
https://github.com/zyndagj/BSMAPz
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
https://gitlab.com/ezlab/busco
The example configuration file, with paths updated appropriately, is
BUSCO_v3_userguide.pdf (local copy)
http://bio-bwa.sourceforge.net/
The programs are available in the default PATH for all users,
so just type
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
Documentation files included with CAP3
http://www.inra.fr/mia/T/CartaGene/
http://www.inra.fr/mia/T/CartaGene/
Installed to default PATH for all users, type
http://cd-hit.org/
download page is https://github.com/weizhongli/cdhit
Installed to default PATH for all users, type
Complete list of CD-HIT programs:
|
|
|
The programs are available in all users' path, so just type the name of a program
to run it, e.g.
Installation notes for the development version, revision 4358, June 30, 2013
http://sourceforge.net/projects/cdbfasta/
There is a web site, Circoletto at http://bat.ina.certh.gr/tools/circoletto/ which implements a web interface to Circos
http://www.stanford.edu/group/rosenberglab/clumpp.html
CLUMPP_Manual.pdf (local copy)
The program is in the default PATH for all users, type
This program can use multiple processors, use the
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
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
clustalw2 help screen ( from
clustalw2 full help screen ( from
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
http://bozeman.mbt.washington.edu/consed/consed.html
Consed README file, version 23.0
Consed current features
http://www.sanger.ac.uk/resources/software/cnd/
The help screen from
cnD README file = the manual
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
https://github.com/cole-trapnell-lab/cufflinks
The program is in the default PATH for all users
https://cutadapt.readthedocs.io/en/stable/
http://dagchainer.sourceforge.net/
Documentation files
https://bitbucket.org/mkroon/dd_detection
http://edwards.sdsu.edu/cgi-bin/deconseq/deconseq.cgi
https://github.com/tobiasrausch/delly
http://www.netlab.uky.edu/p/bioinfo/DiffSplice
Program is installed in the default PATH for all users
Instructions are on this page
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.
https://software.broadinstitute.org/software/discovar/blog/
http://www.stanford.edu/group/rosenberglab/distruct.html
Manual (local copy): distructManual.pdf
Publication (local copy): distructNote.pdf
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.
http://www.niehs.nih.gov/research/resources/software/biostatistics/eagleview/"
The program is available to all users in the "Bioinformatics" menu
https://github.com/zachcp/ea-utils/
http://www.biostat.wisc.edu/~kendzior/EBSEQ/
Commands to prepare the R environment:
library(blockmodeling)
library(EBSeq)
https://www.ncbi.nlm.nih.gov/books/NBK179288/
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.
A list of all EMBOSS programs
"USA" Documentation
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.
The source code files for version 5.2 were dated April 27, 2004
A link to the original publication (pdf)
http://estscan.sourceforge.net/
Local copy of documentation user_guide_fev_07.pdf dated 2007-02-20
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
http://faculty.virginia.edu/wrpearson/fasta/
Manual fasta_guide.pdf (local copy)
https://github.com/dcjones/fastq-tools
https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
Available in the "Bioinformatics" menu on all servers
http://genome.sph.umich.edu/wiki/FastQValidator
https://github.com/OpenGene/fastp
http://cmpg.unibe.ch/software/fastsimcoal2/
Installation is just copy the binary
http://rajanil.github.io/fastStructure/
http://hannonlab.cshl.edu/fastx_toolkit/
https://sourceforge.net/projects/fcgene/
fcgene-1.0.7.pdf (local copy)
http://www.bioinfo.ufpr.br/fgap/
A simpler launcher is provided.
You can use the program
Manual, obtained by running fgap without any parameters
usage.txt
Sample files can be found in
Included README file
http://tree.bio.ed.ac.uk/software/figtree/
Example files
http://www.agcol.arizona.edu/software/fpc/
Available in the "Bioinformatics" menu on all servers
https://github.com/ekg/freebayes
The gene ontology tables have been installed to
README file
func.html
func-refin.html
Manual pages can be accessed with
http://www.baseclear.com/bioinformatics-tools
GapFiller v1-10 is installed in the default PATH for all users.
The program name is:
Documentation files included with the program are in
See also related program Topoview
http://compbio.cs.brown.edu/projects/gasv/
Local copy of included documentation
https://github.com/halelab/GBS-SNP-CROP
http://www.broadinstitute.org/gatk/index.php
A wrapper program called
To get the help screen for an individual program, use
Description, copied from the
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
http://www2.imm.dtu.dk/~gigu/Geneland/
Geneland runs under R, and can be launched with a menu item under the Bioinformatics menu
http://genomica.weizmann.ac.il/
The single main program
http://genome.crg.es/software/gfftools/GFF2PS.html
Local copy of manual converted to pdf format MANUAL_GFF2PS_v0.96.pdf
http://research-pub.gene.com/gmap/
Programs are available in the default PATH for all users
The command
http://bioinfo.unl.edu/gramalign.php
Executable is
https://github.com/PapenfussLab/gridss
Path to executable is
https://sites.google.com/site/gvcftools/
The program is available to all users in the "Bioinformatics" menu
Command-line operation parameters
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
https://github.com/nservant/HiC-Pro
The program
3.1b1 Documentation (pdf)
http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html
http://www-huber.embl.de/users/anders/HTSeq/doc/index.html
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
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
http://www.broadinstitute.org/software/igv/home
The program is available to all users in the "Bioinformatics" menu
http://comailab.genomecenter.ucdavis.edu/index.php/RESCAN
Installed to default PATH, either use full name
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.
https://github.com/ebi-pf-team/interproscan
InterProScan 5 http://code.google.com/p/interproscan/
http://code.google.com/p/interproscan/wiki/Introduction
https://github.com/sauloal/introgressionbrowser
http://www.geneontology.org/GO.annotation.interproscan.shtml Dead link
Binaries and data are located in
The sample command given to test your installation is:
http://bioinfo.bti.cornell.edu/cgi-bin/itak/index.cgi
Local copy of the manual file
To run type
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
http://www.cbcb.umd.edu/software/jellyfish/
The newest version 2.x program
Manual http://www.cbcb.umd.edu/software/jellyfish/jellyfish-manual-1.1.pdf
Local copy jellyfish-manual-1.1.pdf
Runs under Wine as a text interface program, but needs a graphic window. Avaliable in the "Bioinformatics" menu for all users.
Home page: https://github.com/lindenb/jvarkit/
List of programs available: https://github.com/lindenb/jvarkit/wiki/_pages
http://msa.sbc.su.se/cgi-bin/msa.cgi
https://www.bx.psu.edu/~rsharris/lastz/
http://www.cultivatingdiversity.org/software.html
Local copy of documentation UserGuide.pdf
https://github.com/arq5x/lumpy-sv
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:
http://mafft.cbrc.jp/alignment/software/
readme 7.305
http://www.yandell-lab.org/software/maker.html
http://deepc2.psi.iastate.edu/aat/map2/map2.html
web site no longer exists Dec. 11, 2016
map2 is in the default PATH for all users, to use it type
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
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
http://mesquiteproject.org/
and documentation is at http://mesquiteproject.wikispaces.com/
The program is available to all users in the "Bioinformatics" menu
http://www.chibi.ubc.ca/matrix2png/
http://chibba.agtec.uga.edu/duplication/mcscan/
The program executable name is
The helper program
Documentation:
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:
For MCScanX-transposed, there are several programs, use:
For MCScanx (GitHub version), use:
To use MCScanX|x downstream analysis java programs, first execute
or
as appropriate
https://watson.hgen.pitt.edu/docs/mega2_html/mega2.html
http://www.megasoftware.net/index.php
The executable commands are
Output from
https://github.com/voutcn/megahit
http://melt.igs.umaryland.edu/index.php
http://alumni.cs.ucr.edu/~yonghui/mgmap.html
Note that the executable name is
https://github.com/lh3/minimap2
Access the man page with
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
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
http://dogma.ccbb.utexas.edu/mitofy/
Local copy of the manual README.pdf
A public web server implementation is available at /cgi-bin/mitofy/mitofy.cgi
http://johnsonlab.ucsf.edu/mochi.html
The program is available to all users in the "Bioinformatics" menu
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)
http://mrbayes.sourceforge.net/
http://sfu-compbio.github.io/mrsfast/
https://www.mabs.at/ewing/msms/
http://alumni.cs.ucr.edu/~yonghui/mstmap.html
Executable has been renamed to
http://mummer.sourceforge.net/The programs are available in all users' path, so just type the name of a MUMmer program
to run it, e.g.
I have written one supplemental program,
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
The program
Version 3.8.31b is available as
Version 3.8.425 is available as
MUSCLE user guide as a PDF file or as a web page
http://bio-mview.sourceforge.net/index.html
http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/
http://cegg.unige.ch/newick_utils
Installed to default PATH for all users, executable is
http://www.ebi.ac.uk/~zerbino/oases/ Oases Manual in pdf formatThe software is available in a directory which reflects the current version number, e.g.
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.
https://github.com/aubombarely/Organelle_PBA
The program name is
http://www.orthomcl.org/orthomcl/
Included documentation from version 2.0.9
Installation notes version 2.0.9
Installation notes version 1.2
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
or type the following alias for the above command
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.
https://people.sc.fsu.edu/~dswofford/paup_test/
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
https://code.google.com/p/pbsim/
http://www.exelixis-lab.org/pear
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.
http://stephenslab.uchicago.edu/software.html#phase
Instructions: instruct2.1.pdf
The program, accessible in the default PATH, is
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:
For convenience, and if 4 gigabytes is adequate, you can use the wrapper program
https://github.com/broadinstitute/pilon/wiki
Installation notes
http://gmt.genome.wustl.edu/pindel/current/
The programs
Installation notes
http://pipmaker.bx.psu.edu/pipmaker/
Installation notes
http://plantgrn.noble.org/PlantTFcat/
Command line backend pipeline is called with full path
Backend pipeline usage
Notes: Input FASTA must not contain blank lines, corresponding error message is
http://evolution.gs.washington.edu/phylip.html
Local copy of included documentation
http://platanus.bio.titech.ac.jp/
Publication in Genome Research
README file version 1.2.4 local copy (version number 1.2.3 internally)
There is a wrapper program that loads needed libraries, type
http://pngu.mgh.harvard.edu/~purcell/plink/
Version 1.90
http://royfrancis.github.io/pophelper/
http://derisilab.ucsf.edu/software/price/index.html
The program is installed in the default PATH, type
A local copy of the program documentation: index.html
And the readme file included with the program:
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
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
A web interface is available at Primer3Plus
http://prinseq.sourceforge.net/
http://prinseq.sourceforge.net/manual.html#STANDALONE
The programs
The PRINSEQ README file
Output from
Output from
Supplied example: example/example1.html
http://research.haifa.ac.il/~ssagi/software/
A launcher for R is available in the bioinformatics menu.
Type
type
https://github.com/njdbickhart/RAPTR-SV
Documentation (local copy)
http://sco.h-its.org/exelixis/web/software/raxml/index.html
https://github.com/chrisamiller/readdepth
There is a set of programs to help make annotations, createCustomAnnotations.
These programs
the README file for createCustomAnnotations programs: README
http://iubio.bio.indiana.edu/soft/molbio/readseq/java/
Type
Note that there is also a different program installed named
This program also has a graphic interface version built in, this version is available in the "Bioinformatics" menu
http://www.sanger.ac.uk/resources/software/reapr/
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
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
http://repeatexplorer.umbr.cas.cz/
Output from
http://www.cbs.dtu.dk/services/RNAmmer/
Manual: Rnnotator2.3Manual.pdf
The program is installed in
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.
See the Roche instructions page
http://deweylab.biostat.wisc.edu/rsem/
Documentation README for RSEM
Installed in the default PATH for all users
https://github.com/najoshi/sabre
Readme file: README.md
https://github.com/GregoryFaust/samblaster
Local copy of SAMBLASTER_Supplemental.pdf
http://samstat.sourceforge.net/
http://samtools.sourceforge.net/
Note that the default version is 0.1.19. To run the newer 1.xx version, execute this command
prior to running
The SAM Format Specification (pdf)
Installation notes for SAMtools version 0.1.19
Installation notes for SAMtools version 1.xx
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
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
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
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
This program was written by Indraniel Das, web site http://indraniel.wordpress.com/2010/04/23/sff2fastq/
This program will convert a Roche
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
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
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
http://compbio.cs.toronto.edu/shrimp/
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
http://www.cbs.dtu.dk/services/SignalP/
https://github.com/popgenmethods/smcpp
Installation notes for virtual machine, version 2.0.1
Installation notes for virtual machine, version 2.2
Installation notes for SMRT Link
http://korflab.ucdavis.edu/software.html
http://chibba.pgml.uga.edu/snphylo/
The program
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
http://snpomatic.sourceforge.net/
The program
Link to manual (PDF)
Manual included with program Manual.doc
Documentation for "SOAPaligner/soap2" is a man page, type
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
ReadMe file for SOAPec
Installation notes for SOAPsnp
readme file for SOAPsnp
Installation notes for SOAPindel
readme file for SOAPindel
Installation notes for GapCloser
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
http://splicegrapher.sourceforge.net/
http://www.phylogenetic-networks.org/
http://zombie.cb.k.u-tokyo.ac.jp/sprai/index.html
Software page at NCBI: http://www.ncbi.nlm.nih.gov/Traces/sra/?view=software
Programs have been installed in the default PATH for all users, just type
the name to use it, e.g.
http://www.baseclear.com/bioinformatics-tools
SSPACE standard v3.0 is installed in the default PATH for all users.
The program name is:
The program name is:
Documentation files included with the program are in
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
http://creskolab.uoregon.edu/stacks/
Documentation:
https://github.com/alexdobin/STAR/releases
The exectuable is
The manual pdf STARmanual.pdf
Local copy STARmanual.pdf
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
The web interface is at http://taylor0.biology.ucla.edu/structureHarvester/
The Python script has been installed locally, available in the default PATH:
The README file:
The
http://subread.sourceforge.net/
Manual included with the program: SubreadUserGuide.pdf
Programs are installed in the default PATH for all users
http://www.agcol.arizona.edu/software/symap/
The program is available to all users in the "Bioinformatics" menu
http://bioinf.scri.ac.uk/tablet/
The program is available to all users in the "Bioinformatics" menu
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
in your script
An undocumented change to TASSEL4 standalone
(Tassel Version: 4.3.7 Date: April 17, 2014),
the plugin
I saved some helpful output from this new plugin as
From Tassel4-standalone: TasselPipelineCLI.pdf
Tassel 5 command line documentation
http://svdetect.sourceforge.net/Site/Home.html
README file (local copy)
Manual (SVDetect web site)
The programs
http://sourceforge.net/projects/svdetection
The programs
README file from sourceforge page
http://svmerge.sourceforge.net/
Manual SVMerge_Documentation.pdf
http://www.ncbi.nlm.nih.gov/genbank/tbl2asn2
To get the installed version number type
https://github.com/jhrf/telomerecat
http://compbio.dfci.harvard.edu/tgi/software/
Software download page is http://sourceforge.net/projects/tgicl/
For documentation type
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.
https://github.com/nstenz/TICR
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"
http://www.jmüller.name/treegraph/
Local copy of documentation docu.pdf
Local copy of sample files
http://treegraph.bioinfweb.info/
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
https://github.com/hall-lab/svtyper
https://github.com/samtools/tabix
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
The new version is available as
Installation notes for TIGRA-SV 0.1
Installation notes for TIGRA 0.3.7
http://ccb.jhu.edu/software/tophat
The program is in the default PATH for all users
http://flybase.org/static_pages/docs/software/topoview.html
http://transdecoder.github.io/
https://bitbucket.org/nygcresearch/treemix/wiki/Home
Documentation treemix_manual_2_14_12.pdf
http://www.usadellab.org/cms/index.php?page=trimmomatic
A wrapper for the java program is
Pass as the first parameter either
The remaining parameters are as documented on the home page
https://github.com/trinityrnaseq/trinityrnaseq/wiki
The programs are not in the default PATH, find them at the version-independent symbolic link
The programs are not in the default PATH, find them at the version-independent symbolic link
http://lowelab.ucsc.edu/tRNAscan-SE/
man page:
Online manual: http://lowelab.ucsc.edu/tRNAscan-SE/Manual/Manual.html
Available in "Bioinformatics" menu
Installed to default PATH for all users, type
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.
https://github.com/BGI-shenzhen/VCF2Dis
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
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.
For transcriptomic assembly Velvet is extended by Oases.
https://github.com/torognes/vsearch
http://research.haifa.ac.il/~ssagi/software/
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
http://research.haifa.ac.il/~ssagi/software/
http://www.lge.ibi.unicamp.br/zorro/
The two programs are