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Category bioinformatik.de / Software / Unix / 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/

BIONJ: an improved version of the NJ algorithm.
http://www.crt.umontreal.ca/~olivierg/bionj.html

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/

CONSEL: a program for assessing the confidence of phylogenetic tree selection.
http://www.is.titech.ac.jp/~shimo/prog/consel/

Darwin stands for Data Analysis and Retrieval With Indexed Nucleotide/peptide sequences.
http://cbrg.inf.ethz.ch/Darwin/index.html

DiAlign2 - multiple alignment of DNA or protein sequences.
http://www.gsf.de/biodv/dialign.html

Genetics Computer Group (GCG)- Software for the Analysis of Genes and Proteins
http://www.accelrys.com/about/gcg.html

PAL: Phylogenetic Algorithms Library. PAL focuses on probabilistic data modelling, providing, e.g., routines for maximum-likelihood analysis and probability models for nucleotide/protein substitution.
http://www.cebl.auckland.ac.nz/pal-project/history.html

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

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

PHYLO_WIN is a graphic tool for molecular phylogenetic inferences.
http://pbil.univ-lyon1.fr/software/phylowin.html

PSeq-Gen - Protein Sequence-Generator: An application for the Monte Carlo simulation of protein sequence evolution along phylogenetic trees.
http://evolve.zoo.ox.ac.uk/software/PSeq-Gen/main.html

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

ROSE: Random-model Of Sequence Evolution. Rose implements a new probabilistic model of the evolution of RNA-, DNA-, or protein-like sequences.
http://bibiserv.TechFak.Uni-Bielefeld.DE/rose/

Seq-Gen - Sequence-Generator: An application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees.
http://evolve.zoo.ox.ac.uk/software/Seq-Gen/main.html

SeqEvolver simulates the evolution of a collection of protein or DNA sequences, with user-defined substitution rates and evolution time.
http://fasta.bioch.virginia.edu/seqevolver/

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

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

TOPAL package for detecting Recombination - The TOPAL package checks for evidence of past recombination events, by looking for changes in the inferred phylogenetic tree TOPology between adjacent regions of a multiple sequence ALignment.
http://www.bioss.sari.ac.uk/~frank/Genetics/topal.html

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

TreeView X - A phylogenetic tree viewer for Linux and Unix.
http://darwin.zoology.gla.ac.uk/~rpage/treeviewx/

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/