A console-based sequence alignment viewer
Project description
alv: a command-line alignment viewer
View you DNA or protein multiple-sequence alignments right at your command line. No need to launch a GUI!
Features:
- Command-line based, no GUI, so easy to script viewing of many (typically small) MSAs.
- Reads alignments in FASTA, Clustal, PHYLIP, 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.
Examples
Quick viewing of a small alignment:
alf msa.fa
This autodetects sequence type (AA, DNA, RNA, coding DNA), colors the sequences, and formats the alignment for easy viewing in your terminal.
View three sequences, accessions a
, b
, and c
, from an alignment:
alf -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.
Install
Recommended installation is with pip install alv
.
For developers
Run python setup.py develop test
for development install and to execute tests.
Project details
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