Pinned Repositories
ABC
Approximate Bayesian Computation on hybrid simulations - subsumed into HybridSim. The 'main' for HybridSim is here.
BeastLieMarkov
Beast 2 plugin implementing the distingished pair Lie Markov models of DNA evolution
biojavaExtensions
Reusable code extending the capabilities of Biojava 1.8.4. (Old version because I'm using Nexus parsing, which didn't make it to later Biojava versions.)
bisse
R code for BiSSE paper Ketelaar Jones et al.
HybridSeq
Simulates phylogeny with reticulation and produces sequences. Subsumed into the HybridSim program.
HybridSim
The HybridSim program plus manual
HybridStats
Summary statistics on gene trees over a fixed set of taxa. Subsumed into HybridSim program.
IQ-TREE
Efficient phylogenetic software by maximum likelihood
mdwUtils
Miscellaneous code I use in multiple projects, not dependent on third party libraries (such as PAL or BioJava)
pal-1.5.1
Phylogenetics Applications Library, version 1.5.1. THIS IS NOT MY WORK.
MichaelWoodhams's Repositories
MichaelWoodhams/BeastLieMarkov
Beast 2 plugin implementing the distingished pair Lie Markov models of DNA evolution
MichaelWoodhams/ABC
Approximate Bayesian Computation on hybrid simulations - subsumed into HybridSim. The 'main' for HybridSim is here.
MichaelWoodhams/biojavaExtensions
Reusable code extending the capabilities of Biojava 1.8.4. (Old version because I'm using Nexus parsing, which didn't make it to later Biojava versions.)
MichaelWoodhams/bisse
R code for BiSSE paper Ketelaar Jones et al.
MichaelWoodhams/HybridSeq
Simulates phylogeny with reticulation and produces sequences. Subsumed into the HybridSim program.
MichaelWoodhams/HybridSim
The HybridSim program plus manual
MichaelWoodhams/HybridStats
Summary statistics on gene trees over a fixed set of taxa. Subsumed into HybridSim program.
MichaelWoodhams/IQ-TREE
Efficient phylogenetic software by maximum likelihood
MichaelWoodhams/mdwUtils
Miscellaneous code I use in multiple projects, not dependent on third party libraries (such as PAL or BioJava)
MichaelWoodhams/pal-1.5.1
Phylogenetics Applications Library, version 1.5.1. THIS IS NOT MY WORK.
MichaelWoodhams/pal-mdw
A modified version of the Phylogenetics Analysis Library (PAL, 1.5.1)
MichaelWoodhams/palExtensions
palExtensions
MichaelWoodhams/stomata
Code for stomata paper