Software & Data


Java applications

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.

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

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.

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

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

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

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 "+".

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.

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

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 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.