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arvestad/alv: v1.3.0 — the official JOSS release

Lars Arvestad

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.


  • 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.

This is the release that corresponds to what is published in JOSS.
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