# Output formats

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).

## plain

A simple multiple sequence alignment format.

MView option: `-out plain`

This is composed of rows of identifier and sequence in two columns like:

    id1   sequence1
    id2   sequence2
    id3   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 input sequences need not be aligned vertically, but they must all be the same length. Use `-` and/or `.` characters for gaps.

## mview

An annotated multiple sequence alignment format (the default).

MView option: `-out mview`

This is composed of rows of row number, identifier, annotations and sequence in multiple columns like:

    num1 id1 annotation1a annotation1b ... sequence1
    num2 id2 annotation2a annotation2b ... sequence2
    num3 id3 annotation3a annotation3b ... sequence3

with the same restraints as `plain` format. The annotation columns are things like percent coverage, percent identity, sequence description, orientation, etc., and vary with input data source.

## FASTA

The classic FASTA (or Pearson) sequence file format.

MView option: `-out fasta` or `-out pearson`.

## CLUSTAL/aln

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.

## PIR

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.

## MSF

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.

## RDB

MView option `-out rdb`

A tab-separated format including scoring information. RDB is a CSV-style format with header lines giving column name and type information (see rdb).