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of the Department of Zoology, The Natural History Museum, London, U.K.

(,, and aresome of the many tributes to the late Ross Crozier).

APE: analyses ofphylogenetics and evolution in R language.

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It canread and write trees, allows many kinds of annotation of nodes, rearrangementand editing of the tree, addition of multiple bootstrap values, collapsingof nodes, and more.

DIPLOMO: The tool for anew type of evolutionary analysis.

TREECON: a software package forthe construction and drawing of evolutionary trees.
It can be downloaded fromat of the Department of Genome Sciencesof the University of Washington, Seattle, Washingtonhas released AMBIORE(Applications for Mcmc Bayesian Inference Of Rates in Evolution),version 1.00, which estimates rates of change in nucleotide sequences depending on the two neighboring bases.

 

A simulation test bed for hypothesesof genome evolution.

boundaries of the source trees are specified (as nexus-format CHARSETs).
The evolutionary model allows substitution rates at a site to depend on the two flanking nucleotides, the branch of the phylogenetic tree, and position within a sequence.

of the Institut des Sciences de l'Evolution of theUniversité de Montpellier, France,along with K.
For the purposes of this list, the relevant feature is its abilityto compute a variety of genetic distance measures includingof Jukes and Cantor, the Kimura2-parameter distance, and the Tamura-Nei distance, each of thesewith or without correction for gamma-distributed rates of evolution.


Estimating the rate of evolution of the rate of molecularevolution.

It then calculates measure of departure of these changes frommodels of uniform neutral substitution, with respect to differentproperties of the amino acids.

Estimating the rate of evolution of the rate of molecular evolution.

It also allows construction and plottingof "reticulograms" that show departures from treelike structure, andinteractive manipulation of the tree and reticulogram diagrams.

A problem-solving Approach to the teaching of evolution.

of the Life Science Research Centerof Kagawa University, Japan(),Masastoshi Nei of the Institute of Molecular and Evolutionary Geneticsof the Department of Biology.

The user chooses some rate parameters and the number of species.

Pennsylvania State University, University Park,Pennsylvania, and Koichiro Tamura of Tokyo Metropolitan University, Tokyo,Japanhave released POPTREE2, whichcomputes various genetic distance measures and constructstrees of populations or closely related species from genefrequency data by using the Neighbor-Joining method and UPGMA.

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Themethods available include Sattath and Tversky's ADDTREE method,Nei and Saitou's Neighbor-Joining method, Gascuel's UNJ UnweightedNeighbor-Joining method, his BIONJ method, theCircular order reconstruction method of Makarenkov and Leclerc(1997), and Yushmanov (1984),and the MW weighted least-squares method by Makarenkov (1997) andMakarenkov and Leclerc (1998).

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of the Service d'Eco-Ethologie Evolutiveat the the Université Libre de Bruxelles, Brussels, Belgiumdistribute SPAGeDi(Spatial Pattern Analysis of Genetic Diversity),version 1.3, a program to compute a variety of different genetic diversity andgenetic distance statistics.