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

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.

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.