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WINIPAUP 1.0 Paup Windows Interface software
Phylip 3.695 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 3.0b 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.
Archaeopteryx 0.9901 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
COMPONENT 2.0 program for analysing evolutionary trees
NJplot 2.4 a tree drawing program able to draw any phylogenetic tree
MEGA 6.0.6 Molecular Evolutionary Genetics Analysis
TreeSAAP 3.2 Selection on Amino Acid Properties
mesquite 2.75 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 4.13.1 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 2.6 a program for the calculation of the statistics and associated P-values for the nested clade analysis (NCA) developed by Templeton and collaborators.
RDP 4.46 Beta Recombination detection program
FastME 2.0.7 a distance based phylogeny reconstruction algorithm.
T-REX 4.01 Tree and Reticulogram reconstruction
FSTAT a computer package for PCs which estimates and tests gene diversities and differentiation statistics from codominant genetic markers
ProfDist 0.9.9 Beta 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
PVT Phylogenetic Visualization tool
PHASE 2.0 a software package for PHylogenetics And Sequence Evolution
BAMBE 4.01a Bayesian Analysis in Molecular Biology and Evolution
jMODELTEST 2.1.7 phylogenetic model averaging
ModelPie 1.01 a windows and linux interface for modeltest.
Clann 3.2.3 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 v3.16b a java implementation of the evolutionary trace method
NimbleTree 2.6 program for making phylogenetic trees starting from sequence data
Phylogen 1.1 implements some straight-forward birth-death models for simulating phylogenies
BEAST 2.2.1 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 07/2008 a comprehensive phylogenetic tree visualization and manipulation software
DNATREE 1.3 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 2006 a program for building and displaying phylogenetic trees
MrBayes 3.2.5 a program for the Bayesian estimation of phylogeny,
Network 4.613 software for generating evolutionary trees and networks ,
PhyDE 0.9971 Phylogenetic Data Editor
PRAP 2.0b3 software for Parsimony ratchet analyses with PAUP.
CopyCat 2.03 provides an easy and fast access to cophylogenetic analyses
Dendroscope 3.2.10 An interactive viewer for large phylogenetic trees
TreeGraph 2.4.0-456 beta A graphical editor for phylogenetic trees.
SeqState 1.41 Primer design and sequence statistics for phylogenetic DNA data sets
CDTree 3.1 A tool to aid in the classification & evolutionary relationships of protein sequences.
TreeDyn 198.3 Dnamic graphics and annotations for phylogenetic or classification trees analyses .
Baobab 3.31 An editor for large phylogenetic trees written in Java.
Bosque 2.0 alpha A graphycal software to perform phylogenetic analyses.
DoubleTree 0.7 An application for comparing two trees using coupled interaction.
figtree 1.4.2 A graphical viewer of phylogenetic trees.
DensiTree 2.2.1 A program for qualitative analysis of sets of trees.
Leaphy 1.0 Likelihood estimation algorithms in phylogenetics.
Phylodendron 0.8d Phylogenetic tree drawing.
RASP 3.2 Reconstruct Ancestral State in Phylogenies



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