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Welcome to, an online notebook for Ian Holmes' research group at the University of California, Berkeley.


Information about the group.



  • Address: 381 Stanley Hall, University of California, Berkeley, CA 94720-3220.
  • Phone: (510) 666 - 2791.



Links to software developed by the group.

Genome informatics


JBrowse is a JavaScript genome browser. Fast, portable, and secure, it's used by thousands of sites including a large number of model organism projects.

Apollo, the online curation platform, is built on top of JBrowse:


Biomake is a port of GNU Make that allows MD5 signatures, job submission to queues, multiple wildcards per rule, and logic programming extensions.

Molecular evolution


Historian is a program for ancestral sequence reconstruction, using phylogenetic Markov chain models of substitutions and indels. In our tests (as of 2016) it's the most accurate tool for reconstructing ancient sequences and rates.


xrate is software for fitting structured phylogenetic models to multiple sequence alignments. It's been used to estimate many substitution models, including these ones:

It can also be used to fit structured phylogenetic grammars to multiple alignments, e.g. as described here:

And it can do ancestral sequence reconstruction:

Some more links:


stemloc is software for simultaneous alignment and folding of RNA.

Other bioinformatics tools

File formats

The lab provides several tools for manipulating standard bioinformatics file formats:

DNA storage

dnastore is software for encoding and decoding information in DNA sequences using error-tolerant codes that are robust to insertions, deletions and duplications

Gene ontology

wtfgenes is software implementing the MCMC method of Bauer _et al_ for gene set analysis using the Gene Ontology

Oxford nanopore

quaff is a Pair HMM for aligning Oxford nanopore reads.

Non-bioinformatics tools


figlet-js is a JavaScript implementation of figlet by Scott Gonzalez. We have added to it some animation effects and an interactive demo.

Procedural graphics

facesjs is a JavaScript library by Jeremy Scheff for generating vector-based cartoon faces. We have added to the facial feature repertoire and included some basic affect modeling.

Interactive fiction

Boswell is an experimental IDE for authoring and hosting multi-player choice-based interactive fiction.

Wiki migration

This wiki was hosted for many years using TWiki. For various mundane reasons we eventually moved it to Mediawiki. To do this we modified a script originally written by Ryan Castillo. Our updated version of this script is linked below.


Random rants on this wiki.

Essays on algorithms and applications

Collections of links to papers

Teaching pages

Opinion pieces