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A console-based sequence alignment viewer

Project description

# alv: a command-line alignment viewer

View your DNA or protein multiple-sequence alignments right at your command line. No need to launch a GUI!

Note: alv requires Python v3.4 or later. Earlier versions may also work, but this has not been tested.

### Features

  • Command-line based, no GUI, so easy to script viewing of many (typically small) MSAs.
  • Reads alignments in FASTA, Clustal, PHYLIP, NEXUS, and Stockholm formats.
  • Output is formatted to suit your terminal. You can also set the alignment width with option -w.
  • Can color alignments of coding DNA by codon’s translations to amino acids.
  • Guesses sequence type (DNA/RNA/AA/coding) by default. You can override with option -t.
  • Order sequence explicitly, alphabetically, or by sequence similarity.
  • Restrict coloring to where you don’t have indels or where there is a lot of conservation.

## Install

Recommended installation is: ` pip install --upgrade pip pip install alv `

If you have a half-modern BioPython installed, Python v3.4 _should_ work. BioPython is a dependency and will only get installed automatially with pip install alv if you are using Python v3.6 or later, because BioPython was apparently not on PyPi before that.

## Examples

Quick viewing of a small alignment: ` alv msa.fa ` This autodetects sequence type (AA, DNA, RNA, coding DNA), colors the sequences, and formats the alignment for easy viewing in your terminal. When applying alv to an alignment of coding DNA, the coding property is autodetected and colors are therefore applied to codons instead of nucleotides. ![Seven coding DNA sequences](https://github.com/arvestad/alv/raw/master/doc/screenshot_2.png)

View three sequences, accessions a, b, and c, from an alignment: ` alv -so a,b,c msa.fa `

Feed alignment to less, for paging support. ` alv -k msa.fa | less -R ` The -k option ensures that alv keeps coloring the alignment (by default, piping and redirection removes colors), and the -R option instructs less to interpret color codes.

## For developers

Run python setup.py develop test for development install and to execute tests.

## Screenshots

### Full PFAM domain

All of the sequences in PFAM’s seed alignment for PF00005

![PF00005 seed MSA](https://github.com/arvestad/alv/raw/master/doc/screenshot_PF00005.png)

### Yeast sequences from PF00005

Using the option -sm YEAST, we reduce the alignment to the ones with a matching accession.

![Small MSA from PF00005](https://github.com/arvestad/alv/raw/master/doc/PF00005_yeast.png)

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