Phylogenetic

Bio::Tree::Compatible is a Perl module for testing compatibility of phylogenetic trees with nested taxa. SYNOPSIS use Bio::Tree::Compatible; use Bio::TreeIO; my $input = new Bio::TreeIO(-format => newick, -file => input.tre); my $t1 = $input->next_tree; my $t2 = $input->next_tree; my...

Bio::Phylo::IO Perl module contains input and output of phylogenetic data. SYNOPSIS use Bio::Phylo::IO; # parsing a tree from a newick string my $tree_string = (((A,B),C),D);; my $tree = Bio::Phylo::IO->parse( -string => $tree_string, # old parser, always adds node labels -format =>...

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

TreeViewJ is an open source, cross-platform tool for viewing and analyzing phylogenetic trees. It provides the user with the capability to rename, color, and adjust the width of nodes and branches to produce publication-quality images. If dates are available for taxa, the software can map them...


Platforms: Mac

PhyloWidget is a program for viewing, editing, and publishing phylogenetic trees online. It is small, contains a simple yet powerful user interface, and contains many novel features not available in other phylogenetic viewers. PhyloWidget is specifically designed for: * Visually exploring...


Platforms: Mac

SEMPHY is a tool for data-intensive phylogenetic reconstruction. SEMPHY infers phylogenies by Maximum Likelihood, the most established criterion for finding the correct phylogenetic tree. SEMPHY searches for both the most likely topology of the evolutionary tree, and the optimal lengths of its...


Platforms: Mac

GeoMeTree is a python program to compute the geodesic path between two phylogenetic trees. Further details on the algorithm and the use of the program can be found in the manual (pdf).


Platforms: Mac

A modular software framework for phylogenetic analysis and visualization. Existing phylogenetic software can be split into two groups. Algorithmic packages that provide computational methods for a specific problem, and visualization tools to analyze results. Many algorithmic tools lack in...


Platforms: Mac

Probability of Synapomorphy was designed as an R script that implements a new method for evaluating synapomorphy on phylogenetic trees. All you have to do is install R and run the script. A method that quantifies the pattern of character state distribution over a cladogram and as such is free...


Platforms: Windows

Primrose is a simple, Java based application designed to help you identify potentially useful oligonucleotides for use as probes or PCR primers as phylogenetic tools.


Platforms: Windows

Toolkit to examine the topology of a phylogenetic tree, place amino acid substitutions on specific branches, polarize them and compare amino acid sequences of homologous proteins to answer a wide range of questions about protein evolution.


Platforms: Windows, Mac, Linux

JPhylo is a Java based visualization program used to display sequences of phylogenetic trees.


Platforms: Windows, Mac, Linux

PhyloPattern is a Java/Prolog API, helpful to simulate human reading of phylogenetic trees. Bioinformatician can: annotate trees, apply complex patterns to a tree to search specific architectures or extract information, compare trees with dynamically gen


Platforms: Windows, Mac, Linux

PhyloSort sorts phylogenetic trees by searching for user-specified subtrees that contain a monophyletic group of interest defined by operational taxonomic units.


Platforms: Windows, Mac, Linux

A userfriendly graphical front-end for phylogenetic analyses using RAxML (Stamatakis, 2006). Please cite: Silvestro, Michalak (2011) - raxmlGUI: a graphical front-end for RAxML. Organisms Diversity and Evolution. DOI: 10.1007/s13127-011-0056-0


Platforms: Windows, Mac, Linux

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

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

Sequin is a stand-alone software tool developed by the NCBI for submitting and updating entries to the GenBank sequence database. It is capable of handling simple submissions that contain a single short mRNA sequence, and complex submissions containing long sequences, multiple annotations, gapped...


Platforms: Mac

NCBI Genome Workbench is an integrated application for viewing and analyzing sequence data. With Genome Workbench, you can view data in publically available sequence databases at NCBI, and mix this data with your own private data. Genome Workbench can display sequence data in many ways,...


Platforms: Mac

Topiary Explorer is an innovative phylogenetic tree-viewing program written in Java that, unlike most phylogenetic tree-viewing software currently available, integrates the tree along with its related metadata. This tree-metadata relationship facilitates easy identification of interesting...


Platforms: Mac