Ian Holmes's repositories
EvolPairHMM
Evolutionary Pair HMM
safejax
Serialize JAX, Flax, Haiku, or Objax model params with 🤗`safetensors`
TheRing
A song about the anti-horror properties of children
flash-attention-jax
Implementation of Flash Attention in Jax
jaccuse
J'accuse!
llm
Access large language models from the command-line
latex-inputs
LaTeX bibliography
hyena
JAX/Flax implementation of the Hyena Hierarchy
coarse-indel-models
Coarse-grained approach to evolutionary models involving insertions and deletions (indels)
trajectory-likelihood
Calculate indel trajectory likelihoods using methods of MiklĂłs, Lunter & Holmes (2004), De Maio (2020), and Holmes (2020)
ihh.github.io
Holmes lab website
snowclone
Snowclone scraper script.
stockholm-js
Parser for Stockholm format
brokentelephone
Phylogenetic alignment parlor game
JBrowseR-paper
Repo for the paper describing JBrowseR
6502wars
6502-based cellular automata
tree-align-view
A multiple alignment viewer with integrated phylogeny and structure browsing.