CIPRES Software

Links to Software developed by CIPRES team members are shown below.

Analysis:

• 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.
• PHYML a fast algorithm to estimate large phylogenies by maximum likelihood.
• 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.
• NETGEN a phylogenetic network simulator.
• RAxML (Randomized Axelerated Maximum Likelihood) is a program for Maximum Likelihood-based inference of large phylogenetic trees.
• Garli (Genetic Algorithm for Rapid Likelihood Inference)performs heuristic phylogenetic searches under the General Time Reversible (GTR) model of nucleotide substitution.

Display Software

• Dendroscope is an interactive viewer for large phylogenetic trees; interactive browsing, editing, and export of trees in multiple file formats in publication quality.

Community Software

Here we provide a link to Felsenstein's compendium of software relevant to the Phylogenetics/Systematics.

phyloXML • an XML language for phylogenies

AMAP a fast and accurate amino acid multiple sequence alignment program that utilizes posterior decoding, and a novel sequence annealing alignment method.

CIPRES is a Collaboration of the Following Institutions:
American Museum of Natural History, Florida State University, New Jersey Institute of Technology, North Carolina State University, Rice University, San Diego Supercomputer Center, Texas A&M, University of Arizona, University of British Columbia, University of California at Berkeley, University of California at San Diego, University of Connecticut, University of Pennsylvania, Univ. of South Carolina, University of Texas at Austin, and Yale University. xhtml | css