Software & Data

Software

Java applications

CodonSplit
Ho SYW (2011) Version 1.0. University of Sydney, Australia.
CodonSplit takes an alignment of a protein-coding gene and produces three output files, one with each of the codon positions.

SiteSampler
Ho SYW (2010) Version 1.1. University of Sydney, Australia.
SiteSampler can sample the sites of a sequence alignment to produce replicate data sets.

Sequescence
Ho SYW (2007) Version 1.0. University of Oxford, UK.
Sequescence simulates the appearance of miscoding lesions as a result of post-mortem damage in ancient DNA.

RateEvolver
Ho SYW (2005) Version 1.1. University of Oxford, UK.
RateEvolver simulates the evolution of the substitution rate on a fixed nine-taxon tree. It allows the rate to vary among branches in either an autocorrelated or uncorrelated manner.

R scripts

ClockstaR
Duchêne S, Molak M, & Ho SYW (2013)
ClockstaR selects the number of relaxed clocks for multigene datasets.

DataPartitioning
Duchêne S (2012)
DataPartitioning takes a long alignment of concatenated genes or partitions (e.g., a mitogenome) and exports individual alignments for each partition.

RemoveRedundantTaxa
Duchêne S (2012)
RemoveRedundantTaxa is a substitute for a MacClade utility. It removes redundant sequences from an alignment to produce an alignment of unique taxa only. The resulting taxon names are appended with a "+".

TreeSpace
Duchêne S (2012)
TreeSpace takes a long alignment and will generate a 100 bootstrap NJ consensus tree for each user-specified partition. Then the distance between all the trees are calculated, effectively exploring the topologies generated by each partition.

ShuffleSites
Duchêne S (2011)
ShuffleSites takes an alignment, resamples the sites a number of times. It can resample without replacement (shuffle sites) or with replacement (bootstrap).

Python scripts

getRatesLengths
Ho SYW (2013)
getRatesLengths takes an annotated tree file from FigTree and extracts a list of branch lengths and corresponding branch-specific rates. These values can be used for subsequent analyses, such as calculation of average rate weighted by branch length.

Data

Data sets from published research

Alignment of 12 mitochondrial protein-coding genes from 32 cetacean species
Size: 32 taxa x 10,845 bp
Publication: Ho SYW, and Lanfear R (2010) Improved characterisation of among-lineage rate variation in cetacean mitogenomes using codon-partitioned relaxed clocks. Mitochondrial DNA, 21: 138-146.