Phylogenetic Software
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- GRAPPA is a program to infer phylogenies from unichromosomal gene-order and gene-content data.
- POY is a program for cladistics and phylogenetics analysis using sequence and/or morphological data.
- MALIGN is a parsimony-based alignment program for molecular sequences.
- PAUP provides tools for inferring and interpreting phylogenetic trees.
- MacClade is a pioneering program for interactive analysis of evolution of a variety of character types.
- Mesquite is a set of modules in Java to carry out a wide variety of analyses in comparative biology.
- MrBayes is a program for the Bayesian estimation of phylogeny.
- HY-PHY has general ways of enabling the user to perform a wide variety of statistical tests of different models of molecular sequence change.
- Hickory provides for Bayesian estimation of F-statistics from both dominant and co-dominant marker data.
- GDA computes linkage and Hardy-Weinberg disequilibrium, some genetic distances, and provides method-of-moments estimators for hierarchical F-statistics.
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