**Phylogenetics and Phylogeography Softwares**

Phylogenetic analysis by maximum likelihood (PAML)

Yang, Z. 1997 PAML: a program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 13, 555-556.

Yang, Z. 2007 PAML 4: Phylogenetic Analysis by Maximum Likelihood. Mol. Biol. Evol. 24: 1586-1591.

DIYABC (Do It Yourself ABC)

Cornuet, J-M., Pudlo, P., Veyssier, J., Dehne-Garcia, A., Gautier, M., Leblois, R., Marin, J-M., Estoup, A. 2014 DIYABC v2.0: a software to make Approximate Bayesian Computation inferences about population history using Single Nucleotide Polymorphism, DNA sequence and microsatellite data. Bioinformatics. 30: 1187–1189, doi: 10.1093/bioinformatics/btt763.

PopART

PopART includes several network inference methods. Minimum Spanning, Median Joining, and TCS are all popular methods that have been described elsewhere. Ancestral Parsimony, Integer Neighbor-Joining, and Tight Span Walker are new methods that I'll describe briefly here.

TCS

TCS is a Java computer program to estimate gene genealogies including multifurcations and/or reticulations (i.e. networks).

Clement, M., Posada, D. & Crandall, K. 2000. TCS: a computer program to estimate gene genealogies. Molecular Ecology. 9: 1657-1660

BAYESIAN PHYLOGENETICS & PHYLOGEOGRAPHY (BP&P)

Yang, Z. & Rannala, B. 2002. Bayesian species delimitation using multilocus sequence data. PNAS. 107: 9264-9269.

SPREAD: Spatial Phylogenetic Reconstruction of Evolutionary Dynamics

SPREAD is a user-friendly application to analyze and visualize phylogeographic reconstructions resulting from Bayesian inference of spatio-temporal diffusion.

RASP (Reconstruct Ancestral State in Phylogenies)

RASP is a tool for inferring ancestral state using S-DIVA (Statistical dispersal-vicariance analysis), Lagrange (DEC), Bayes-Lagrange (S-DEC), BayArea and BBM (Bayesian Binary MCMC) method.

ALTER (ALignment Transformation EnviRonment)

FaBox (1.41)

FaBox is an intutitive and simple online toolbox for fasta sequences.