CandidatePrograms

Candidate Programs for our Class

Keep in mind that we will definitely not be able to talk about all of them.

• adegenet is an R-package dedicated to the exploratory analysis of genetic data. It implements a set of tools ranging from multivariate methods to spatial genetics and genome-wise SNP data analysis.

• BEDASSLE This is a method I worked on in collaboration with Peter Ralph and Graham Coop. It allows users to quantify the relative contributions of geographic and environmental distance to patterns of genetic differentiation.

• mtml-msBayes msBayes uses hierarchical approximate Bayesian computation (HABC) for comparative (multi-taxa) phylogeographic inference. HABC allows testing hypotheses and estimating hyper-parameters that quantify levels and patterns of congruence across co-distributed taxon-pairs in divergence/colonization times and/or categorical biogeographic histories.

• GPHoCS G-PhoCS is a software package for inferring ancestral population sizes, population divergence times, and migration rates from individual genome sequences. G-PhoCS accepts as input a set of multiple sequence alignments from separate neutrally evolving loci along the genome. Parameter inference is done in a Bayesian manner, using a Markov Chain Monte Carlo (MCMC) to jointly sample model parameters and genealogies at the input loci.

• TESS implements ancestry estimation algorithms for spatial population genetic analyses. The program performs individual geographical assignment, admixture analysis, and can be used to run genome scans for selection. TESS is particularly suited to seeking genetic discontinuities in continuous populations and estimating spatially varying individual admixture proportions.

• STRUCTURE is a free software package for using 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.

• BAPS introduces the spatial clustering model for DNA sequence data such that the output can be displayed on Google Maps.

• Geneland is a computer program for statistical analysis of population genetics data. Its main goal is to detect population structure in form of systematic variation of allele frequency that can be detected from departure from Hardy-Weinberg and linkage equilibrium.

• Structurama is a program for inferring population structure from genetic data. The program assumes that the sampled loci are in linkage equilibrium and that the allele frequencies for each population are drawn from a Dirichlet probability distribution.

• Partition finder is free open source software to select best-fit partitioning schemes and models of molecular evolution for phylogenetic analyses.

(this seems to have a recent spinoff by Frandsen, but his github site pbfrandsen's github needs better organization before diving into this.

• RaXML is a fast maximum likelihood phylogenetic inference program

• SVDquartets is a program to compute a score based on singular value decomposition of a matrix of site pattern frequencies corresponding to a split on a phylogenetic tree. These quartet scores can be used to select the best-supported topology for quartets of taxa, which in turn can be used to infer the species phylogeny using quartet methods. It is implemented in PAUP*

[ http://people.sc.fsu.edu/~dswofford/paup_test/ PAUP*] is the reference phylogeny inference program including a kitchen sink of methods.