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Evolutionary Biology And Biodiversity

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Evolutionary Biology & Biodiversity
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School of Earth & Environmental Sciences
The University of Adelaide
SA 5005 Australia
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Phone: +61 8 8303 3999
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Software

The following software packages were explored throughout the workshop:

	Software Description	Info	Download
1	Arlequin Arlequin is an exploratory population genetics software environment able to handle large samples of molecular data (RFLPs, DNA sequences, microsatellites), while retaining the capacity of analyzing conventional genetic data (standard multi-locus data or mere allele frequency data).	Arlequin	Download Arlequin Version 3.5.1.2
2	Cervus A computer program for assignment of parents to their offspring using genetic markers. Cervus uses likelihood, a well-established statistical method for parentage analysis, to assign parentage.	Cervus	Download Cervus Version 3.0
3	BEST Bayesian Estimation of Species Trees estimates the joint posterior distribution of gene trees and species trees using multilocus molecular data that accounts for deep coalescence but not for other issues such as horizontal transfer or gene duplication.	BEST	Register BEST
4	IM The IM program aims to simultaneously estimate divergence time and immigration rates between two populations.	IM	Download IM
5	POLDISP POLDISP is a software package to make inferences on contemporary pollen dispersal from mapped mother-offspring diploid genotypic data.	POLDISP	Download POLDISP
6	BayesAss Bayesian estimation of recent migration rates using multilocus genotypes.	Bayesass	Apple PC
7	MEGA Molecular Evolutionary Genetics Analysis (MEGA) is an integrated tool for conducting automatic and manual sequence alignment, inferring phylogenetic trees, mining web-based databases, estimating rates of molecular evolution, and testing evolutionary hypotheses.	MEGA	Register MEGA Version 4
8	NM+ Software designed to make inferences on plant gene dispersal and mating patterns by modelling parentage probabilities of offspring based on the spatially explicit neighbourhood model.	NM+	Download NM+
9	PhyBase PhyBase is an R package for phylogenetic analysis of multilocus sequences under the multi-species coalescence model. This package should be uploaded into R (see below) along with Matrix and Ape packages.	PhyBase	Download PhyBase
10	Structure Uses multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals and estimating population allele frequencies in situations where many individuals are migrants or admixed.	Structure	Download Structure Version 2.3.3 with graphical front end
11	R R is `GNU S', a freely available language and environment for statistical computing and graphics which provides a wide variety of statistical and graphical techniques: linear and nonlinear modelling, statistical tests, time series analysis, classification, clustering, etcR	R	Download R * base Binaries for base distribution (managed by Duncan Murdoch)
12	MrBayes MrBayes is a program for the Bayesian estimation of phylogeny.	MrBayes	Download MrBayes

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