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.
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.
