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Phylo-Win Graphical color interface for molecular phylogenetic inference. It performs neighbor-joining, parsimony, and maximum likelihood methods and bootstrap with any of them. http://pbil.univ-lyon1.fr/software/phylowin.html Univ-lyon1.fr  ~   Site Info   Whois   Trace Route   RBL Check   PAML Phylogenetic analyses of DNA or protein sequences using maximum likelihood. http://abacus.gene.ucl.ac.uk/software/paml.html Ucl.ac.uk  ~   Site Info   Whois   Trace Route   RBL Check   Mesquite Experimental, modular software for evolutionary biology, designed to help biologists analyze comparative data about organisms. http://mesquiteproject.org/mesquite/mesquite.html Mesquiteproject.org  ~   Site Info   Whois   Trace Route   RBL Check   PAUP* PAUP is the most widely used package for phylogenetic inference, and now implements maximum likelihood and distance methods as well as various forms of parsimony. Powerful and very easy to use, particularly the Mac version. http://paup.csit.fsu.edu/ Fsu.edu  ~   Site Info   Whois   Trace Route   RBL Check   Clann: Software for Supertree Methods Clann implements a large number of supertree methods for reconstructing phylogenies from sets of input phylogenetic trees. http://bioinf.may.ie/software/clann/ May.ie  ~   Site Info   Whois   Trace Route   RBL Check   MrBayes Open source software for estimation of phylogenies using Bayesian inference. http://mrbayes.csit.fsu.edu/ Fsu.edu  ~   Site Info   Whois   Trace Route   RBL Check   NONA Freeware software for phylogenetic analyses using parsimony. http://www.cladistics.com/aboutNona.htm Cladistics.com  ~   Site Info   Whois   Trace Route   RBL Check   3I - Internet-accessible Interactive Identification Program to create internet-accessible interactive taxonomic keys. http://ctap.inhs.uiuc.edu/dmitriev/ Uiuc.edu  ~   Site Info   Whois   Trace Route   RBL Check   r8s Open source software for estimating absolute rates of molecular evolution and divergence times on phylogenetic trees. http://loco.biosci.arizona.edu/r8s/ Arizona.edu  ~   Site Info   Whois   Trace Route   RBL Check