A console-based sequence alignment viewer
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!
alv requires Python v3.4 or later. Earlier versions may also work, but this have not been tested.
- 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
- 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
- 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.
Quick viewing of a small alignment:
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
c, from an alignment:
alf -so a,b,c msa.fa
Feed alignment to
less, for paging support.
alv -k msa.fa | less -R
-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.
Recommended installation is with
pip install alv.
If you have a half-modern BioPython installed, 3.4 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.
python setup.py develop test for development install and to execute tests.
Full PFAM domain
All of the sequences in PFAM's seed alignment for PF00005
Yeast sequences from PF00005
Using the option
-sm YEAST, we reduce the alignment to the ones with a matching accession.
Seven coding DNA sequences
alv is autodetecting that the given DNA sequences are coding and therefore colors codons instead
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
|Filename, size & hash SHA256 hash help||File type||Python version||Upload date|
|alv-1.2.0-py3-none-any.whl (18.2 kB) Copy SHA256 hash SHA256||Wheel||py3||Aug 30, 2018|
|alv-1.2.0.tar.gz (16.6 kB) Copy SHA256 hash SHA256||Source||None||Aug 30, 2018|