Phylogeny

MrBayes is a simple, easy to use application specially designed for the Bayesian estimation of phylogeny. The program takes as input a character matrix in a NEXUS file format. The output is several files with the parameters that were sampled by the MCMC algorithm. MrBayes can summarize the... Platforms: Windows

Phight - a phylogeny tree building program Currently, it supports Likelihood method and distance method. This program will includes diagnostic function as a special feature. Platforms: Windows, Mac, Linux

MISFITS is a program to evaluate the goodness of fit of a model to an alignment in phylogeny reconstruction. It offers a look back at the alignment to pinpoint to site patterns that do not fit to the model and the resulting tree (thereafter referred to as the tree-model). MISFITS then introduces... Platforms: Mac

t2prhd is a Perl script which generates simple diagrams that highlight relationships of sequence repeats detected by using a profile HMM in two sequences. Homology relations are identified on the basis of the phylogeny of repeats. Platforms: *nix

FFP (Feature frequency profile) is an alignment free comparison tool for phylogenetic analysis and text comparison. It can be applied to nucleotide sequences, complete genomes, proteomes and even used for text comparison. Features . Comparison of Genomes, protein and nucleic acid sequences... Platforms: *nix

DNATREE is a computer program that simulates the branching of an evolutionary tree, using a model of random branching of lineages. It then evolves a DNA sequence along this tree, and displays the resulting sequences. The user can save the tree and the sequences if they want to use them in other... Platforms: Windows

DNATREE is a computer program that simulates the branching of an evolutionary tree, using a model of random branching of lineages. It then evolves a DNA sequence along this tree, and displays the resulting sequences. The user can save the tree and the sequences if they want to use them in other... Platforms: Linux

DNATREE is a computer program that simulates the branching of an evolutionary tree, using a model of random branching of lineages. It then evolves a DNA sequence along this tree, and displays the resulting sequences. The user can save the tree and the sequences if they want to use them in other... Platforms: Mac

A set of programs for multiple sequence alignment and analysis. The programs use an expandable user interface which allows the addition of external analysis functions without any rewriting of code. The system supports several data types, nucleic and amino acid sequences, text, and masking... Platforms: Mac

t2prhd is a Perl script which generates simple diagrams that highlight relationships of sequence repeats detected by using a profile HMM in two sequences. Homology relations are identified on the basis of the phylogeny of repeats. Platforms: Windows, Mac, Linux

Seqlib is a Python module and application package for population genetics (and more). It allows processing, analyzing and simulating biological sequences. It is specifically designed for automated large-scale sequence analysis. Main features: * Fasta-centered input and output, format... Platforms: Mac

SIMMAP 1.5 is a post tree analysis GUI software package for stochastically mapping mutations on phylogenies. This approach does not rely on parsimony and, therefore, does not suffer some of the serious drawbacks of that method. It uses the "indirect" mutational mapping approach as first developed... Platforms: Mac