Software
IEE researchers have produced numerous software packages for evolutionary analysis from sequence alignment to phylogenetic analysis to pedigree reconstruction.
See summary details and links to relevant websites with more information and downloads below.
4273π
By Daniel Barker, Heleen Plaisier et al
The 4273π project releases materials for teaching and learning bioinformatics, including an SD card image for the low-cost Raspberry Pi computer. This is tailored for bioinformatics use and includes open educational resources for computational biology.
LVB
By Daniel Barker et al
LVB uses parsimony to reconstruct phylogeny from a nucleotide multiple alignment, using a simulated annealing heuristic search. This is suitable for large data matrices.
MCALIGN
By Peter Keightley, Jun Wan and Toby Johnson
Alignment of noncoding DNA sequences based on explicit models of indel evolution
MLGENOMEU
By Peter Keightley
Estimation of mutation parameters from mutation accumulation experiments.
DFE-alpha
By Peter Keightley and Adam Eyre-Walker
Inference of the distribution of fitness effects of new mutations and the fraction of adaptive substitutions (alpha) based on nucleotide polymorphism frequency spectra and between-species nucleotide divergences.
PARTIGENE
By Mark Blaxter et al
Partigene is a suite of transcriptomics analysis tools.
Other software for phylogenetic analysis is also available from the Blaxter lab’s website
BEAST
By Alexei J. Drummond & Andrew Rambaut
BEAST is a cross-platform program for Bayesian MCMC analysis of molecular sequences orientated towards rooted, time-measured phylogenies or genealogies inferred using relaxed molecular clock models. It can be used as a method of reconstructing phylogenies and demographic histories but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology.
Numerous other software packages for phylogenetic analysis are also available from the Rambaut lab’s website
PEDANTIX
By Michael Morrissey
PEDANTICS is a set of software tools, written by Michael Morrissey for facilitating power and sensitivity analyses of quantitative genetic studies of natural populations.
CERVUS
By Tristan Marshall
Cervus is a computer program for assignment of parents to their offspring using genetic markers. Cervus represents an easy-to-use and practical tool for scientists seeking to establish parent-offspring relationships even when some genotypes are incomplete, incorrect or missing.
MasterBayes
By Jarrod Hadfield
MasterBayes uses MCMC techniques to integrate over uncertainty in pedigree configurations estimated from molecular markers and phenotypic data. Emphasis is put on the marginal distribution of parameters that relate the phenotypic data to the pedigree. MasterBayes is an R library, but all simulation is done in compiled C++ for efficiency.
MCMCglmm
By Jarrod Hadfield
MCMCglmm is an R package for fitting Generalised Linear Mixed Models using Markov chain Monte Carlo techniques. MCMCglmm is an R library.