Links
"From the genome to the tree of life"
Publications Research Centers Databases Societies Software Deep Gene Participants

 Genetics / Genomics Software
 
Societies
 
An Alphabetic List of Genetic Analysis Software
Extensive list of analysis software
 
Genetics/Genomics Software links at Dendrome
 Phylogenetics Software
 
Software Lists
ANU Bioinformatics Software List
A small list of software for analysis of nucleic acid sequences, including the RAPDistance and DIPLOMO packages
Clustering and Multivariate Analysis
A short review of classification software maintained by CSNA
EP-GED Software
Lists both phylogenetics software and population and quantitative genetics software. Brought to you by EP-GED, the Evolution and Population Genetics Educational Database.
Paul Harvey research group at Oxford University
This site includes an archive of phylogenetic analysis and simulation software, mostly formatted for the Macintosh, and much of it developed by the research group.
Internet Directory for Botany: Software
This mammoth list includes phylogenetic and taxonomic software, along with applications in collections management, ecology, conservation, horticulture and education. Both commercial and non-commercial programs are listed.
Laboratoire de Biométrie, Génétique et Biologie des Populations
This CNRS research group, based at Lyon University in France, offers several databases and programs for nucleotide sequence retrieval and analysis, as well as for multivariate statistical and phenetic analysis. Also available through anonymous FTP.
Mick's Software Links
Extensive list of biology-related software, including phylogenetics, molecular sequence editing and alignment, graphics, statistics and quite a lot else.
Morphometrics Software at SUNY
Lists of programs useful for morphometrics, the analysis of shape and form
European EMBnet Node
This node in the European Molecular Biology Network offers access to a variety of services, databases, and software, including a list of phylogeny programs available commercially or as shareware.
Parsimony Analysis Software
Software listings maintained by the Hennig Society
Phylogeny Programs Listings
Maintained by J. Felsenstein, this is a rather extensive listing of software, most of which is available on-line. There is a good deal of information about each program, and the list is organized by program type.
Ribosomal Database Project
Includes short list of useful software
Slatkin Lab Genetics Software
Software developed by members of Dr. Montgomery Slatkin's lab at UC Berkeley. This includes several phylogenetics-related programs, as well as software for population biology and modelling evolutionary processes.
Software Listing at Glasgow
Extensive and well organized list of software sources and providers, found at Taxonomy and Systematics at Glasgow. The site includes alignment, analysis and interpretive programs.
TIGR Software Tools
Free software for managing and editing molecular data sets, made available by TIGR (The Institute for Genomic Research).
Natural History Museum: Software
A few PC-based software packages, created by Dr. Mark Wilkinson, are available here: PICA95 for compatibility analysis, REDCON for reduced consensus, and TAXEQ2 for taxonomic reduction.
 

Programs

CAIC
Comparative Analysis program based on methods by Pagel and Felsenstein
COMPARE 4.2
Computer programs for the phylogenetic analysis of comparative data
Genetic Data Analysis (GDA)
PC program for analyzing discrete genetic data; the program is currently in its testing phase.
LucID
A Windows-based interactive program for constructing and viewing taxonomic keys. One of several pest management software packages offered at the Australian Cooperative Research Center for Tropical Pest Management.
MacClade
This is one of the premiere software packages for analyzing cladistic results. Available here are a free downloadable demo version, files to upgrade older versions to the latest, a FAQ, a list of known bugs, and ordering information.
PC-RASA
This Macintosh-based shareware program implements a new statistical approach for detecting signal in a phylogenetic dataset.
PDAP
A set of MS-DOS computer programs distributed free of charge. It is a set of phenotypic diversity analysis programs.
PHYLIP
Phylip is a premiere phylogenetics software package. The software is free. Documentation is provided with the software but may also be viewed on the WWW, courtesy of the Institute of Biochemistry and Biophysics of the Polish Academy of Sciences.
R-Package
This free software package carries out various multivariate and phenetic analyses. Although developed primarily for ecological applications, some of its component programs are useful in systematics and biogeography. Available for Mac or VAX systems (a Windows version is planned).
 
 


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