A console-based sequence alignment viewer
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!
alv requires Python v3.4 or later. Earlier versions may also work, but this has not been
Latest feature additions
If you have more than one alignment in your input file, then the first alignment is output unless you use the --alignment-index (-ai) option to choose another.
alvis now adapted for use in Python notebooks (tested on Jupyter) through two convenience functions 'view' and 'glimpse'. Both functions take a BioPython alignment object and outputs a view of the alignment.
from Bio import AlignIO msa = AlignIO.read('PF00005.fa', 'fasta') import alv alv.view(msa)
in a Jupyter notebook cell and evaluating will yield a colored alignment in the
For large alignments, the glimpse function is convenient since a subset of the alignment, selected as an easily detected conserved region, is shown.
Look for more usage information view
help(alv.view)in a notebook cell.
- 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, from file or
- 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.
- Focus on variable columns with the options
--only-variable-excluding-indels, contributed by nikostr, that constrains coloring to columns with variation and variation not counting indels.
- The command
alv -g huge_msa.fadisplays cut-out of the MSA, guaranteed to fit one terminal page without scrolling or MSA line breaking, that is supposed to give you an idea of alignment quality and contents.
alv -r 20 huge_msa.fato get a view of the MSA containing only 20 randomly selected sequences.
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.
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.
alv to an alignment of coding DNA, the coding property is autodetected and colors are therefore applied to codons instead
View three sequences, accessions
c, from an alignment:
alv -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.
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.
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