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| Phylogenetics
Software |
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| 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.
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Programs
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- 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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