Software (7)
ClustalX // Clustal X is a new windows interface for the ClustalW multiple sequence alignment program. It provides an integrated environment for performing multiple sequence and profile alignments and analysing the results. The sequence alignment is displayed in a window on the screen. A versatile coloring scheme has been incorporated allowing you to highlight conserved features in the alignment. The pull-down menus at the top of the window allow you to select all the options required for traditional multiple sequence and profile alignment
GSF: The Genetic Software Forum // Provides a forum for posting questions and answers about the use of software for genetic analysis including (but not limited to) PAML, MrBayes, Immanc and BayesAss.
MacClade // A computer program for phylogenetic analysis written by David Maddison and Wayne Maddison. Its analytical strength is in studies of character evolution. It also provides many tools for entering and editing data and phylogenies, and for producing tree diagrams and charts.
Mesquite // Software for evolutionary biology, designed to help biologists analyze comparative data about organisms. Its emphasis is on phylogenetic analysis, but some of its modules concern population genetics, while others do non-phylogenetic multivariate analysis. Because it is modular, the analyses available depend on the modules installed. Analyses include: Reconstruction of ancestral states (parsimony, likelihood); Tests of process of character evolution, including correlation; Simulation of character evolution (categorical, DNA, continuous); Parametric bootstrapping (integration with programs such as PAUP* and NONA); Morphometrics (PCA, CVA, geometric morphometrics); Coalescence (simulations, other calculations); Tree comparisons and simulations (tree similarity, Markov speciation models)
Online ClustalW alignment // Clustal W is a general purpose multiple sequence alignment program for DNA or proteins. It produces biologically meaningful multiple sequence alignments of divergent sequences. It calculates the best match for the selected sequences, and lines them up so that the identities, similarities and differences can be seen. Evolutionary relationships can be seen via viewing Cladograms or Phylograms.
PHYLIP // A free package of programs for inferring phylogenies. It is distributed as source code, documentation files, and a number of different types of executables. These Web pages, by Joe Felsenstein of the Department of Genome Sciences at the University of Washington, contain information on PHYLIP and ways to transfer the executables, source code and documentation to your computer.
Phylogeny programs // Joe Felsenstein's comprehensive listing of phylogeny packages. No attempt has been made to exclude programs that do not meet some standard of quality or importance. Updates to these pages are made about twice a year (Note -- there were no updates of these pages from early 2001 until August, 2003. Updating has now resumed and should be complete before the end of 2003.).
