Phylogenetic |
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| PAUP |
Phylogenetic Analysis Using Parsimony |
| Phylip
3.67
|
the PHYLogeny Inference Package |
| TreeView
1.6.6 |
a simple program for displaying phylogenies |
| GeneTree
1.3 |
an experimental program for comparing gene and species trees. |
| NDE 0.5.0 |
NEXUS Data Editor) is a program to create and edit NEXUS format data files |
| TreeMap 1.0 |
an experimental program for comparing host and parasite trees |
| Phyltools
1.32 |
a freeware utilities package that works with the phylogenetic inference package Phylip |
| tree-puzzle
5.2 |
a computer program to reconstruct phylogenetic trees from molecular sequence data by maximum likelihood. |
| ATV
4.0a5 |
a Java tool for the visualization of annotated phylogenetic trees |
| TREECON
1.3b Demo |
a software package developed primarily for the construction and drawing of phylogenetic trees |
| ProBiosys
0.9 |
has been designed to enabled in depth analysis and comparison of disparate data sets which would be difficult to achieve with stand-alone programs. |
| COMPONENT
2.0 |
program for analysing evolutionary trees |
| NJplot |
a tree drawing program able to draw any phylogenetic tree |
| MEGA
4.0 |
Molecular Evolutionary Genetics Analysis |
| TreeSAAP 3.2 |
Selection on Amino Acid Properties |
| mesquite 2.0 |
software for evolutionary biology |
| PAL 1.51 |
Analysis Library A Java library for molecular evolution and phylogenetics |
| Vanilla 1.2 |
a collection of command line programs written in Java to access some selected features in PAL |
| SplitsTree 4.8 |
application for computing evolutionary networks from molecular sequence data. |
| TCS 1.21 |
a Java computer program to estimate gene genealogies including multifurcations and/or reticulations (i.e. networks). |
| GEODIS 2.5 |
a program for the calculation of the statistics and associated P-values for the nested clade analysis (NCA) developed by Templeton and collaborators. |
| RDP 3b22 |
Recombination detection program |
| FastME 1.0 |
a distance based phylogeny reconstruction algorithm. |
| REAP |
an integrated environment for the manipulation and phylogenetic analysis |
| T-REX 4.01 |
Tree and Reticulogram reconstruction |
| FSTAT 2.9.3.2 |
a computer package for PCs which estimates and tests gene diversities and differentiation statistics from codominant genetic markers |
| ProfDist 0.9.7 |
A tool for the construction of large phylogenetic trees based on profile distances |
| STC 1.2 |
a new distance-based clustering method, triplet clustering algorithm |
| SymmeTREE |
tests of differential diversification rates |
| PVT |
Phylogenetic Visualization tool |
| TREEFINDER 200706 |
computes phylogenetic trees from molecular sequences. |
| PHASE 2.0 |
a software package for PHylogenetics And Sequence Evolution |
| BAMBE 2.01b |
Bayesian Analysis in Molecular Biology and Evolution |
| MODELTEST 3.7 |
program for the selection the model of nucleotide substitution that best fits the data. |
| MTgui 1.5 |
a windows and linux interface for modeltest. |
| Clann 3.02 |
determining the optimal phylogenetic supertree |
| Phylogenetic Independence 2.0 |
to conduct the Test For Serial Independence (TFSI) on continuously valued characters and the Runs Test on discretely valued characters (Abouheif 1999) |
| Jevtrace2 v3.12b |
a java implementation of the evolutionary trace method |
| NimbleTree 2.6 |
program for making phylogenetic trees starting from sequence data |
| Phyl-O-Gen 1.1 |
implements some straight-forward birth-death models for simulating phylogenies |
| BEAST 1.4.6 |
cross-platform program for Bayesian MCMC analysis of molecular sequences |
| MESA 1.9.23 |
Macroevolutionary Analysis & Simulation |
| TreeJuxtaposer 2.1 |
Compare phylogenetic evolutionary trees interactively and automatically |
| TreeExplorer 2.12 |
display a phylogenetic tree in several different styles |
| TreeMe 03/2007 |
a comprehensive phylogenetic tree visualization and manipulation software |
| DNATREE 1.2 |
a computer program that simulates the branching of an evolutionary tree |
| Genie 3.0 |
Genealogy Interval Explorer |
| Pebble v1.0 |
Phylogenetics, Evolutionary Biology, and Bioinformatics in a moduLar Environment |
| ArboDraw |
a program for building and displaying phylogenetic trees |
| PhyloDraw 0.82 |
a drawing tool for creating phylogenetic trees. |
| MrBayes 3.1.2 |
a program for the Bayesian estimation of phylogeny, |
| Network 4.201 |
software for generating evolutionary trees and networks , |
| PhyDE 0.993 |
Phylogenetic Data Editor |
| PRAP 1.21 |
software for Parsimony ratchet analyses with PAUP. |
