genotypst

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, genome maps, 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 genotypst package:

#import "@preview/genotypst:0.9.0": *

You can perform a simple pairwise alignments and visualize both the alignment and its dynamic programming matrix:

// Perform a local alignment of two DNA sequences
#let dna_alignment = align-seq-pair(
  "AAT",
  "AACTTG",
  match-score: 3,
  mismatch-score: -1,
  gap-penalty: -1,
  mode: "local",
)

// Render the alignment
#render-pair-alignment(
  dna_alignment.seq-1,
  dna_alignment.seq-2,
  dna_alignment.traceback-paths.at(0),
)

// Render the dynamic programming matrix
#render-dp-matrix(
  dna_alignment.seq-1,
  dna_alignment.seq-2,
  cell-values: dna_alignment.dp-matrix.scores,
  path: dna_alignment.traceback-paths.at(0),
  arrows: dna_alignment.dp-matrix.arrows,
)

Read a FASTA file containing a multiple sequence alignment:

// 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 135
#context {
  set text(size: 0.85em)
  render-msa(protein_msa, start: 100, end: 135, 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 135
#render-sequence-logo(sequences, start: 100, end: 135)

To render a genomic locus, you can pass an array of genomic features to the render-genome-map function:

// Render a genome map containing five features
#let locus = (
  (start: 400, end: 1260, strand: 1, label: [A], color: rgb("#56B4E9")),
  (start: 1300, end: 2200, strand: 1, label: [B]),
  (start: 2250, end: 3460, strand: -1, label: [C], color: rgb("#E69F00")),
  (start: 3500, end: 3800, label: [D]),
  (start: 3850, end: 5400, strand: 1, label: [E]),
)

#render-genome-map(
  locus,
  coordinate-axis: true,
  width: 80%,
)

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-rectangular-tree(tree)