*Lagrange* is a [http://www.python.org Python] package implementing likelihood models for geographic range evolution on phylogenetic trees, with methods for inferring rates of dispersal and local extinction and ancestral ranges. This software implements methods described in [http://www.informawor...

Phyutility (fyoo-til-i-te) is a command line program that performs simple analyses or modifications on both trees and data matrices. Makes use of JADE (PEBLS) and JEBL libraries. Please see the [NEWS] page for info concerning updates, etc. *Please use this citation when using Phyutility* [http://...

http://www.atgc-montpellier.fr/phyml PhyML is a software that estimates maximum likelihood phylogenies from alignments of nucleotide or amino acid sequences. It provides a wide range of options that were designed to facilitate standard phylogenetic analyses. The main strengths of PhyML lies in th...

P4 is a Python package that does maximum likelihood and Bayesian phylogenetic analyses on molecular sequences. It's specialty is that you can use heterogeneous models, where the model parameters can differ in different parts of the tree, or over different parts of the data. P4 was written by Peter G...

=HashRF= *Phylogenetic reconstruction techniques are primarily based on computational heuristics and often produce a large number of candidate evolutionary trees. It is necessary to have an efficient method to take these trees as input and return the relationship among them. We design a hash-ba...

=HashCS= *Consensus trees are a popular approach for summarizing the shared evolutionary relationships in a collection of trees. Many popular techniques such as Bayesian analyses produce results that can contain tens of thousands of trees to summarize. We develop a fast consensus algorithm ca...

This is the source code repository for a project named PhyML+M3L. To learn about PhyML+M3L, please go here first: http://phylo.uoregon.edu/software/phyml+m3l/ PhyML+M3L is an extension of PhyML version 3.0, using publicly-available open source C code. The '+M3L' extensions implement several u...

SPRIT - Subtree Prune and Regraft Identification Tool Identifying SPRs in rooted binary phylogenetic trees. See included README for details. Some stand alone python software from the p4 project http://code.google.com/p/p4-phylogenetics/ - THOR, leaf stability measures, maximum, difference...

==What is Phylomel== Phylomel is a project aiming at providing a phylogenetics trees inferring system. To this purpose, it is distributed as a library and binaries. It is easy to integrate with a website, for example. ==Status== Alpha state, but there is already a good amount of documenta...

PHLAWD (pronounced flawd) allows for the creation of large (mega) phylogenies using NCBI databases. Currently the code requires biopython and MYSQL. The package will also include a web-interface in the near future. The first trees using this method are in press. <img src="http://lh3.ggpht.com/_c0...