Instead of the pretty display output, MView can write several useful multiple alignment formats.
Any row or column filtering options will be respected, so you can also extract subsets of sequences (see Filtering rows), or particular alignment blocks or strand oriented data from blast or similar (see the various sequence database search input formats).
A simple multiple sequence alignment format.
MView option: -out plain
This is composed of rows of identifier and sequence in two columns like:
identifier1 sequence1 identifier2 sequence2 identifier3 sequence3
and can contain comment lines starting with #. Identifiers and sequences must not contain any whitespace as this is used to separate the columns. The sequences need not be aligned vertically, but they must all be the same length. Use - and/or . characters for gaps.
The classic FASTA (or Pearson) sequence file format.
MView option: -out fasta or -out pearson.
The CLUSTAL multiple sequence alignment format (version 2.1, as produced by clustalx-2.1).
MView option: -out clustal or -out aln.
Output includes end of row numbers and a Clustal-style *:. amino acid conservation line: * for full column identity, and : or . for strong and weak amino acid grouping, respectively, as defined in CLUSTAL.
For DNA or RNA sequences, if the molecule type was set to nucleic acid with -moltype na or dna or rna, then the clustal conservation line will show only the column identities.
The Protein Information Resource sequence file format.
MView option: -out pir
This format includes a molecule type annotation. If the -moltype option is set (one of aa, dna, rna, na), MView will try to output a reasonable value (P1, DL, RL, XX; for protein, linear DNA, linear RNA, or unknown, respectively). The default is protein.
The Wisconsin Package GCG Multiple Sequence File format.
MView option: -out msf
This format includes a molecule type annotation. If the -moltype option is set (one of aa, dna, rna, na), MView will output the right value (P or N; for protein or nucleic acid). The default is protein.