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!
Note: alv
requires Python v3.x.
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.
Screenshot
Full PFAM domain
All of the sequences in PFAM's seed alignment for PF00005
Ten peptide sequences from PF00005
Seven coding DNA sequences
alv
is autodetecting that the given DNA sequences are coding and therefore colors codons instead
of nucleotides.
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