Software · Brown Lab

Software development

Under the hood

What four of our tools actually do, with the commands to run them.

Rust · Bioinformatics 2025

tidk

Finding the ends of chromosomes

Telomeres are short repeats at chromosome ends, but which repeat varies between lineages. tidk explore discovers the unit de novo, search maps it in windows along every chromosome, and ends checks whether an assembly is telomere-to-telomere.

It runs in seconds on a gigabase genome, and has been run across more than 3,400 Darwin Tree of Life assemblies to build a curated database of telomeric repeats by clade.

$ conda install -c bioconda tidk
# discover the repeat unit
$ tidk explore --minimum 5 --maximum 12 genome.fa
# map it along every chromosome, then plot
$ tidk search --string TTTAGGG --output euphrasia --dir out genome.fa
# telomere-to-telomere check
$ tidk ends --min-sequence-length 1000000 -o euphrasia genome.fa

TTTAGGG (forward)CCCTAAA (reverse)

Schematic of tidk search output for one 30 Mb chromosome in 300 kb windows. Strand-specific repeats spike at each end, plus a small interstitial telomeric sequence. Hover a bar for counts.

Rust · graph algorithms

gfatk

Untangling mitochondrial assembly graphs

Plant mitochondria recombine across repeats, so assemblers return a graph, not a sequence. gfatk reads these GFA graphs, separates mitochondrion from plastid, and finds a linear path that uses every segment as many times as its coverage suggests.

Its ideas went on to underpin Oatk, now a widely used de novo organelle assembler.

$ gfatk stats mito.gfa -t
$ gfatk extract-mito assembly.gfa | gfatk linear > mito.fa
$ gfatk dot mito.gfa | dot -Tsvg > mito.svg

u1 (unique)u2 (unique)

Schematic. Two unique segments joined by a repeat seen at twice the coverage. The animated walk traverses the repeat twice, giving one 468 kb sequence.

Rust · Wellcome Open Research 2023

goat-cli

Asking questions of the whole tree of life

Genomes on a Tree (GoaT) holds genome size, chromosome number and sequencing status for every eukaryote. The command-line client turns a one-line question into an API query, so you can survey thousands of species from the shell.

The chart is built from the same API: every measured plant genome size in eight orders, 5,164 species in all.

# which plants have genomes over 100 Gb?
$ goat-cli taxon search -t Liliales -d --tax-rank species -e 'genome_size > 1e11'
# how many flowering plants have chromosome-level assemblies?
$ goat-cli taxon count -t Magnoliopsida -d --tax-rank species -e 'assembly_level = chromosome'

Live data from the GoaT API (October 2026): measured genome sizes on a log scale. Each row shows up to 110 species, and medians use all 5,164. The European mistletoe genome is one we are working on.

JavaScript · D3

lwPhylo

Phylogenies for the web

A lightweight library that turns a Newick string into rectangular, radial or unrooted layouts for D3. It draws every tree figure on our Figures page.

This is the library itself, running live. Switch layouts, grow a new random tree, or click an internal node to rotate its clade.

import { randomTree } from "@euphrasiologist/lwphylo";
import drawPhylogeny from "@euphrasiologist/lwphylo/draw";

const tree = randomTree(28);
drawPhylogeny(tree, {
  layout: "radial", container: "#tree",
  rotateOnClick: true,
});

Loading lwPhylo…

Live lwPhylo 1.5.1, loaded from npm. Hover a branch to see its root-to-tip distance.

Genomics

All genomics tools

tolkit/tidk Bioinformatics, 2025

Telomere identification toolkit. Discovers and maps telomeric repeats across whole genomes, built to survey the thousands of assemblies coming out of the Darwin Tree of Life.

$ conda install -c bioconda tidk

Rust★ 180

genomehubs/goat-cli Wellcome Open Res, 2023

Command line interface for Genomes on a Tree. Query genome size, chromosome number, assembly status and sequencing-project metadata for any taxon across eukaryotes.

Rust★ 14

c-zhou/oatk Genome Biology, 2025

De novo assembly of complex plant mitochondrial and plastid genomes from HiFi reads. Co-developed with Chenxi Zhou and Richard Durbin.

C★ 89

tolkit/gfatk

A Graphical Fragment Assembly toolkit for plant organelles. Uses graph algorithms to resolve tangled mitochondrial and chloroplast assembly graphs into linear sequences.

Rust★ 17

tolkit/fasta_windows In production at Sanger

Fast sliding-window statistics (GC content, entropy, k-mer statistics) over FASTA files. Runs in production in the Wellcome Sanger Institute's Tree of Life pipelines.

Rust★ 15

Ecology & statistics

Networks, trees and mixed models

Euphrasiologist/oxygraphis

An ecological graph library and CLI for bipartite host–parasite networks, now being applied to field data on wild British eyebrights.

Rust

Euphrasiologist/lwPhylo

A lightweight, low-level JavaScript library for drawing interactive phylogenies from Newick files in a range of layouts.

JavaScript★ 1

Euphrasiologist/VCVglmm

Convenience functions to extract and manipulate variance–covariance matrices from lme4 and MCMCglmm random effects.

R

Approach

How we build software

Research code should outlive the paper it was written for. We aim for tools that are installable in one line, documented, tested and fast enough to run across entire genome collections rather than a handful of samples.

Beyond the packages above, recent work includes inverted-repeat detection, annotation of plant mitochondria and plastids, codon-aware alignment conversion, GFF statistics and transposable element alignment.

Languages: Rust, Python, R, JavaScript, SQL and the shell.

Open tools for open science