ihh

graphgram

Graph grammar library

bracery

Procedural text generator, somewhat compatible with Tracery

trajectory-likelihood

Calculate indel trajectory likelihoods using methods of Miklós, Lunter & Holmes (2004), De Maio (2020), and Holmes (2020)

abrowse

Multiple sequence alignment browser

tree-align-view

A multiple alignment viewer with integrated phylogeny and structure browsing.

carder

Lightweight wrapper to Gajus Kuizinas' Swing for building card-swiping interactive fiction on the web.

stockholm-js

Parser for Stockholm format

evoldeeds

EvolPairHMM

Evolutionary Pair HMM

ihh.github.io

Holmes lab website

6502wars

6502-based cellular automata

augurbot

biochoon

brokentelephone

Phylogenetic alignment parlor game

coarse-indel-models

Coarse-grained approach to evolutionary models involving insertions and deletions (indels)

flash-attention-jax

Implementation of Flash Attention in Jax

hornswaggle

hyena

JAX/Flax implementation of the Hyena Hierarchy

ipip

jaccuse

J'accuse!

JBrowseR-paper

Repo for the paper describing JBrowseR

latex-inputs

LaTeX bibliography

llm

Access large language models from the command-line

picaro

safejax

Serialize JAX, Flax, Haiku, or Objax model params with 🤗`safetensors`

scallywag

snowclone

Snowclone scraper script.

sokoscript

TheRing

A song about the anti-horror properties of children

triax