## 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.

- angsd: Analyses of nextgen sequencing data.

- ASTRAL is a Java program for estimating a species tree given a set of unrooted gene trees. ASTRAL is statistically consistent under multi-species coalescent model (and thus is useful for handling ILS). It finds the tree that maximizes the number of induced quartet trees in the set of gene trees that are shared by the species tree.

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

- BEAST2 is a cross-platform program for Bayesian phylogenetic analysis of molecular sequences. It estimates rooted, time-measured phylogenies using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology.

- 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.

- DADI implements methods for demographic history and selection inference from genetic data, based on diffusion approximations to the allele frequency spectrum. One of ∂a∂i's main benefits is speed: fitting a two-population model typically takes around 10 minutes, and run time is independent of the number of SNPs in your data set. ∂a∂i is also flexible, handling up to three simultaneous populations, with arbitrary timecourses for population size and migration, plus the possibility of admixture and population-specific selection.

- Eigensoft The EIGENSOFT package implements methods from the following 2 papers: Patterson et al. 2006 PLoS Genet 2:e190 (population structure); Price et al. 2006 Nat Genet 38:904-9 (EIGENSTRAT stratification correction)

- ExaBayes ExaBayes is a software package for Bayesian tree inference. It is particularly suitable for large-scale analyses on computer clusters. {see MrBayes

- 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.

- GARLI Genetic Algorithm for Rapid Likelihood Inference is a program for inferring phylogenetic trees. Using an approach similar to a classical genetic algorithm, it rapidly searches the space of evolutionary trees and model parameters to find the solution maximizing the likelihood score. It implements nucleotide, amino acid and codon-based models of sequence evolution, and runs on all platforms. The latest version adds support for partitioned models and morphology-like datatypes.

- 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.

- Genepop on the Web and Genepop Software This software calculates standard population genetic quantities, such as FST, isolation by distance measures etc.
- M Raymond and F Rousset. GENEPOP (version 1.2): population genetics software for exact tests and ecumenicism. Journal of Heredity, 86(3):248–249, 1995a.
- M Raymond and F Rousset. An exact test for population differentiation. Evolution, 49(6):1280–1283, Jan 1995b.
- F. Rousset. Genetic differentiation and estimation of gene flow from F-statistics under isolation by distance. Genetics, 145(4):1219–28, 1997.
- F Rousset. GenePop’007: a complete re-implementation of the GenePop software for Windows and Linux. Molecular Ecology Resources, 8(1):103–106, 2008.

- IMa was developed for the fitting of an isolation model with migration to haplotype data drawn from two closely related species or populations.

- MIGRATE Migrate estimates effective population sizes, past migration rates, and divergence times between n population.

- MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. MrBayes uses Markov chain Monte Carlo (MCMC) methods to estimate the posterior distribution of model parameters.

- 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.

- 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.)

- PAUP* is the reference phylogeny inference program including a kitchen sink of methods.

- RaXML is a fast maximum likelihood phylogenetic inference program

- RevBayes Bayesian phylogenetic inference using probabilistic graphical models and an interactive language. Successor of MrBayes.

- 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.

- 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.

- STRAW:STAR,MP-EST, NJst The species tree reconstruction webserver consists of a series of phylogenetic tools for estimating species trees from phylogenomic data: 1) rooting gene trees with outgroup species, 2) estimating species trees from the rooted gene trees using STAR , MP-EST , NJst methods, 3) bootstrap analyses for the species tree reconstruction methods (STAR, MP-EST, and NJst).

- SATE,PASTA,Superfine SATE:Simultaneous Alignment and Tree Estimation (SATé) is a software package for constructing phylogenies and alignments from sequence data; PASTA (Practical Alignment using SATé and TrAnsitivity) is an improvement to SATé: it uses some of the algorithmic design of SATé but is faster, produces more accurate alignments and trees, and can scale to much larger datasets; SuperFine is software for constructing supertrees from source phylogenies.

- 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*

- 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.

- TREEMIX is a method for inferring the patterns of population splits and mixtures in the history of a set of populations. In the underlying model, the modern-day populations in a species are related to a common ancestor via a graph of ancestral populations. We use the allele frequencies in the modern populations to infer the structure of this graph.

- Molecular Evolution workshop software website This site inlcudes many and more of the software mentioned above, check it out.