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Category bioinformatik.de / Software / Windows / Phylogenetic Analysis /

Phylogeny programs cross-referenced by method and system.
http://evolution.genetics.washington.edu/phylip/software.xref.html

ATV - a phylogenetic tree display tool.
http://www.genetics.wustl.edu/eddy/atv/

Clann : Constructing Supertrees from partially-overlapping datasets. The purpose of the program is to implement methods of determining the most suitable phylogenetic supertree, given a set of input source trees.
http://bioinf.may.ie/software/clann/

Compare - for the phylogenetic analysis of comparative data.
http://compare.bio.indiana.edu/

COMPONENT is a computer program for analysing evolutionary trees and is intended for use in studies of phylogeny, tree shape distribution, gene trees/species trees, host-parasite cospeciation, and biogeography.
http://taxonomy.zoology.gla.ac.uk/rod/cpw.html

Diplomo - An interactive computer graphics application for windows that uses the distance plot principle in a new and powerful approach to phylogenetic analysis.
http://life.anu.edu.au/molecular/software/diplomo/

GeneTree is an experimental program for comparing gene and species trees.
http://taxonomy.zoology.gla.ac.uk/rod/genetree/genetree.html

MEGA - Molecular Evolutionary Genetics Analysis.
http://www.megasoftware.net/

PAML - Phylogenetic Analysis by Maximum Likelihood.
http://abacus.gene.ucl.ac.uk/ziheng/paml.html#GetPAML

PAUP*: Phylogenetic Analysis Using Parsimony and other Methods.
http://paup.csit.fsu.edu/

PHYLIP Home Page - Phylogenieprogramm
http://evolution.genetics.washington.edu/phylip.html

Phylodendron is an application for drawing phylogenetic trees, used in evolutionary biology.
ftp://iubio.bio.indiana.edu/molbio/java/apps/trees/phylodendron-doc.html

PhyloDraw is a drawing tool for creating phylogenetic trees.
http://pearl.cs.pusan.ac.kr/phylodraw/

PhyloGrapher is a program designed to visualize and study evolutionary relationships within families of homologous genes or proteins (elements).
http://niblrrs.ucdavis.edu/PhyloGrapher/PhyloGrapher_Welcome.html

PhylPro - Phylogenetic Profiles constitute a novel way of graphically displaying the coherence of the sequence relationships over the entire length of a set of aligned homologous sequences.
http://life.anu.edu.au/molecular/software/phylpro/

RECOMBINE - RECOMBINE fits a model which has a single population of constant size with a single recombination rate across all sites. It can accomodate either plain DNA or RNA data or SNP (Single Nucleotide Polymorphism) data.
http://evolution.genetics.washington.edu/lamarc/recombine.html

SplitsTree: Analyzing and Visualizing Evolutionary Data
http://www-ab.informatik.uni-tuebingen.de/software/splits/welcome_en.html

T-REX performs nine methods of fitting a phylogenetic tree to a given distance matrix containing or not missing values and a method of reconstruction of a reticulation network.
http://www.fas.umontreal.ca/BIOL/Casgrain/en/labo/t-rex/index.html

The PUZZLE Software: Maximum likelihood analysis for nucleotide, amino acid, and two-state data.
http://www.tree-puzzle.de/

TransAlign - A Java program package for aligning coding nucleotide sequences according to the amino acid sequence encoded.
http://life.anu.edu.au/molecular/software/transalign/

TREECON is a software package developed primarily for the construction and drawing of phylogenetic trees on the basis of evolutionary distances inferred from nucleic and amino acid sequences.
http://www.psb.rug.ac.be/bioinformatics/psb/Userman/treeconw.html

TreeDis - A program that finds the patristic distances between all taxa in a phylogenetic tree.
http://life.anu.edu.au/molecular/software/tredis/

TREEFINDER computes phylogenetic trees from DNA sequences. A very fast maximum likelihood program by Gangolf Jobb.
http://www.treefinder.de

TreeMap is an experimental program for comparing host and parasite trees.
http://taxonomy.zoology.gla.ac.uk/rod/treemap.html

TREEVIEW : Tree drawing software for Apple Macintosh and Windows
http://taxonomy.zoology.gla.ac.uk/rod/treeview.html

Weighbor: Weighted Neighbor Joining - Weighbor is a weighted version of Neighbor Joining that gives significantly less weight to the longer distances in the distance matrix.
http://www.t10.lanl.gov/billb/weighbor/