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.
