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Simon Hegele edited this page Apr 19, 2026 · 3 revisions

msa_plot generates plots for pre-computed multiple sequence alignments in FASTA-format.

usage: msa_plot [-h] [-s] [-e] [-r] [-fs] [-cmap] [-cval] [-bl] [-of] msa

Vizualisation of multiple sequence alignments

positional arguments:
  msa                   Multiple sequence alignment (FASTA-format)

options:
  -h, --help            show this help message and exit
  -s , --start          Start of the section you want to show (default: 1)
  -e , --end            End of the section you want to show (default: alignment end)
  -r , --row_length     Number of alignment columns to show per row (default: 100)
  -fs , --font_style    Font style for sequence names ( default: 'normal", choices: ['normal', 'italic', 'oblique'])
  -cmap , --color_map   Choose one of the many colormaps available to matplotlib (default: 'tab20' )
  -cval , --color_val   A character to value map (JSON-format)
  -bl, --bold_last      Highlight last sequence by witing it's name in bold letters
  -of , --out_format    Output format (default: 'png' choices: ['eps', 'jpg', 'jpeg', 'pdf', 'pgf', 'png', 'ps', 'raw', 'rgba', 'svg', 'svgz', 'tif', 'tiff', 'webp'])

Demo plot for some random p53 sequences I found on UniProt and aligned with MAFFT: alt

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