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genotypst is a bioinformatics package for Typst that enables analysis and visualization of biological data. It provides functionality for parsing FASTA and Newick files and generating publication-ready visualizations, including multiple sequence alignments, sequence logos, and phylogenetic trees.

Documentation

Refer to the manual for a comprehensive guide containing examples illustrating how to use genotypst.

Quickstart

A minimal example illustrating the use of genotypst is shown below. To reproduce it, download the example multiple sequence alignment file msa.afa.

In a Typst document, import the package and read the alignment data:

#import "@preview/genotypst:0.1.0": *

// Load sequences
#let sequences = parse-fasta(read("msa.afa"))

// Display the `sequences` variable
#repr(sequences)

(
  "gi|503891280": "MIQRSLRDKQIIKVLTGVRRCGKSTILQMFINFEDLAYEKYDYYELYQYL…",
  "gi|502172365": "TRPRVLRRVMGAVLIDGPKAVGKTQTTTRVLRLDVDVARAALVPEQLFE-…",
  "gi|504805136": "IYPRMDILPNFALVVSGIRRSGKSTLLTQFLNFDTPQLFNFEDFALLDEI…",
  "gi|502700462": "----MLETDLPALLIVGPRASGKTTTAARTVRLDVPAQAAAFDPDAALRN…",
  …
)

A region of the multiple sequence alignment can be rendered with render-msa:

// Render a multiple sequence alignment between positions 100 and 145
#render-msa(sequences, start: 100, end: 145, colors: true, conservation: true)

The same region of the alignment can also be visualized as a sequence logo using render-sequence-logo:

// Render a sequence logo between positions 100 and 145
#render-sequence-logo(sequences, start: 100, end: 145)

You can also use genotypst to parse Newick data and visualize phylogenetic trees:

// Parse Newick data
#let tree = parse-newick(
  "(('Leaf A':0.2,'Leaf B':0.1)'Internal node':0.3,'Leaf C':0.6)Root;"
)
// Render the phylogenetic tree
#render-tree(tree)