Phylip

This package includes a modified version of dnapars.exe from Phylip 3.6. The orignal dnapars,exe uses a menu for settings of parameters. I changed it into a command-line driven one, called mbetoolbox_dnapars.exe. Then I built a MATLAB interface for it. Within MATLAB, after setting the path, set... Platforms: Matlab

PLOTPHYTREE(TREE) renders a phylogenetic tree object into a MATLAB figure as aphylogram with equal angle algorithm.plotphytree(...,'ROTATION',value) will orient the phylogenetic tree within the figure window. Positive angles cause counterclockwise rotation, otherwise clockwise... Platforms: Matlab

Patristic is a Java program that uses as input different tree files and computes their patristic distances. Patristic allows saving and editing in different ways those distances. Patristic provides different graphic views of the results as well as the possibility to save them in the CSV format... Platforms: Mac

TreeStat is an application that can process a set of trees in a PHYLIP or NEXUS format tree file and calculate a number of summary statistics for each. These are saved in a tab-delimited file for analysis in Tracer or statistics packages. A range of summary statistics are included: *... Platforms: Mac

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

BioBrew Linux is an open source Linux distribution that is enhanced for life scientists. It is customized for cluster and bioinformatics computing. It automates cluster installation, includes all the HPC software a cluster enthusiast needs, and contains popular bioinformatics applications.... Platforms: *nix

Bio::Tree::DistanceFactory is a Perl module to construct a tree using distance based methods. SYNOPSIS use Bio::Tree::DistanceFactory; use Bio::AlignIO; use Bio::Align::DNAStatistics; my $tfactory = Bio::Tree::DistanceFactory->new(-method => "NJ"); my $stats =... Platforms: *nix

VLinux Bioinformatics workbench is a Linux distribution for Bioinformatics. It is easy to use, no installation required, CD-based distribution based on Knoppix 3.3. VLinux Bioinformatics Workbench includes a variety of sequence and structure analysis packages. It is an Open source product... Platforms: *nix

CLC Free Workbench is the foundation for all bioinformatics workbenches from CLC bio. This software package is a community edition, available for download free of charge.The workbench creates a software environment enabling users to make basic bioinformatics analyses and smooth data management,... Platforms: Mac

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

SeaView is a multiplatform, graphical user interface for multiple sequence alignment and molecular phylogeny. SeaView reads and writes various file formats of DNA and protein sequences and of phylogenetic trees. SeaView drives programs muscle or clustalw for multiple sequence alignment, and... Platforms: Mac

DendroPy is a Python library for phylogenetic computing. It provides classes and functions for the simulation, processing, and manipulation of phylogenetic trees and character matrices, and supports the reading and writing of phylogenetic data in a range of formats, such as NEXUS, NEWICK, NeXML,... Platforms: Mac

TreeIllustrator is a program for displaying and manipulating phylogenetic trees. It gives you powerful means to customise your phylogenetic trees and compare them with the current classification of organisms. TreeIllustrator was developed as part of The SeqPad software suite,a productivity &... Platforms: Mac

UGENE is a free cross-platform genome analysis suite. It works perfectly on Windows, Mac OS or Linux and requires only a few clicks to install. Features: * Multiple sequence alignment using MUSCLE 3, KAlign, Clustal; * HMM profiles build and search, based on the source of HMMER 2 and HMMER... Platforms: Mac

Script for manipulating tree (*.t, *.trprobs, *.con) and parameter (*.p) files from MrBayes (v.3). The script exctracts trees and (by default) the taxon translation table and the trailing ``end;'' from a MrBayes tree file. A number of options are available: Any contiguous interval of trees can... Platforms: Mac