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Sponsored Links:
Phylodendron (Popularity:  )
http://iubio.bio.indiana.edu/soft/molbio/java/apps/trees/
Java application for drawing phylogenetic trees. Allows you to save in various formats, print, edit, modify, and adorn the tree, and should work on any java runtime platform.
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TreeView (Popularity: )
http://taxonomy.zoology.gla.ac.uk/rod/treeview.html
Simple program for displaying phylogenies.
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Tree Puzzle (Popularity: )
http://www.tree-puzzle.de/
Computer program to reconstruct phylogenetic trees from molecular sequence data by maximum likelihood.
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TAXIS - Taxonomic Information System (Popularity: )
http://www.bio-tools.net/
Database management system for recording taxa, specimens, characters, and images. Also serves as an interactive identification system.
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Phylo-Win (Popularity: )
http://pbil.univ-lyon1.fr/software/phylowin.html
Graphical color interface for molecular phylogenetic inference. It performs neighbor-joining, parsimony, and maximum likelihood methods and bootstrap with any of them.
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PHYLIP (Popularity: )
http://evolution.genetics.washington.edu/phylip.html
Joe Felsenstein's suite of programs implementing perhaps the widest range of phylogenetic inference package. The most widely distributed phylogeny software. Includes distance, likelihood and parsimony methods for a wide range ...
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MacClade (Popularity: )
http://phylogeny.arizona.edu/macclade/macclade.html
A powerful Macintosh package for phylogenetic analysis. Not intended as a stand-alone tool to infer phylogeny, but excels in studying character evolution. Also provides tools for entering and editing data ...
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CAIC (Popularity: )
http://www.bio.ic.ac.uk/evolve/software/caic/index.html
Comparative Analysis via Independent Constrasts. Mac program implementing the independent constrasts method for phylogenetically correct comparative methods.
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ALICE Biodiversity Software (Popularity: )
http://ds.dial.pipex.com/town/square/fd95/
Database management system for managing data about taxa, species, genera, varieties and cultivars.
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TreeMap (Popularity: )
http://taxonomy.zoology.gla.ac.uk/rod/treemap.html
Experimental program for comparing host and parasite trees.
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GeneTree (Popularity: )
http://taxonomy.zoology.gla.ac.uk/rod/genetree/genetree.html
Uses reconciled trees to compare gene trees and species trees, explaining incongruence between the phylogenies by postulating horizontal transfer, gene duplication and loss events. Reprints of papers describing the methods ...
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PAML (Popularity: )
http://abacus.gene.ucl.ac.uk/software/paml.html
Phylogenetic analyses of DNA or protein sequences using maximum likelihood.
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Nona - A Quick Guide to the Commands (Popularity: )
http://www.gwu.edu/~clade/faculty/lipscomb/Nonadoc.html
A brief overview of using Nona for phylogenetic analysis.
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Component (Popularity: )
http://taxonomy.zoology.gla.ac.uk/rod/cpw.html
For analysis of phlyogenies. Includes a wide range of randomisation methods, consensus methods, tree comparison measures, and calculates reconciled trees. Now aging, and available only for Windows machines, but still ...
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DeltaAccess (Popularity: )
http://www.bgbm.fu-berlin.de/projects/DeltaAccess/
A SQL interface to DELTA, implemented in Microsoft Access 97.
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Expert Center for Taxonomic Identification (Popularity: )
http://www.eti.uva.nl/
The Linnaeus II taxonomic content management system supports creating taxonomic databases, computer aided identification keys, interactive biogeographic maps, and literature and glossary databases in one hyperlinked environment.
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Lucid (Popularity: )
http://www.lucidcentral.com/
A system for creating, maintaining, distributing and playing interactive identification keys.
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PaleoTax (Popularity: )
http://www.paleotax.de
The program can give an overview of taxonomic and other information of a taxa group. Recorded data can be assessed or exported as RTF or HTML document.
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Classification Society of North America (Popularity: )
http://www.pitt.edu/~csna/software.html
List of cluster analysis software
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Joe Felsenstein's list of phylogeny programs (Popularity: )
http://evolution.genetics.washington.edu/phylip/software.html
Probably the most comprehensive
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