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[Univ. British Columbia] A program which estimates ancestor states for a continuous trait, and provides a “standard error” for the marginal distribution of each estimate.
[Univ. of Montreal] A phylogenic reconstruction algorithm, which uses an improved version of the NJ algorithm, and is well adapted when evolutionary distances are obtained from aligned sequences.
CAFCA: Collection of APL Functions for Cladistic Analysis
[Leiden Univ.] A program which employs the methods of group-compatibility and component-compatibility to run cladistic analysis of a data matrix.
[Univ. of Oxford] This software implements a suite of phylogenetically comparative methods for data sets including continuous variables.
[Univ. of ALberta] A clustering program that uses single and complete linkage methods to determine the heirarchial clustering for a given data set.
DELTA: Description Language for Taxonomy
[Biodiversity & Biological Collections Server] A method of recording taxonomic descriptions for computer processing, adopted as a standard for data exchange by the International Taxonomic Databases Working Group.
[R.D.M. Page, Univ. of Glasgow] A program for comparing gene and species trees.
[Univ. of Edinburgh] This program uses unweighted parsimony to reconstruct evolution, based on a matrix of discrete characters for different objects. These characters can be aligned DNA , protein sequences, or morphological…
[Maddison & Maddison] (Maddison and Maddison) The analytical strength of MacClade is in studies of character evolution. It also provides many tools for entering and editing data and phylogenies, and for producing tree diagrams and charts.
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[Ziheng Yang] A program package for phylogenetic analyses of DNA or protein sequences using maximum likelihood.
[Indiana University] This is an application for drawing phylogenetic trees.
[Pennsylvania State Univ.] Allows a comparison of phylogenic trees, estimation of the pairwise distances, relative rate tests, and computation of the time of divergence.
[Univ. of Oxford] A program that takes sequential PHYLIP formatted DNA sequences sequences followed by their maximum likelihood phylogeny. It can detect for example, recombination, or gene conversion or convergence.
[Department of Zoology, Univ. of Oxford] Simulates the evolution of protein sequences along evolutionary trees following the procedures previously reported for the DNA sequence simulator Seq-Gen.
[K. Strimmer and A. von Haeseler] This program reconstructs phylogenetic trees from molecular sequence data by maximum likelihood.
[Oxford] An application for estimating the date of divergence between two pairs of sequences given that the date of divergence of the members of each pair is known.
[Ruth Shaw] A program for the maximum likelihood analysis of variance in quantitative genetic data. The programs perform ML or REML on a two generation pedigree with multivariate phenotypic observations and fixed effects.
[Armstrong, Gibbs, Peakall, Weiller] (Australian National University and the Bioinformatics Group) Records and fragment data can be analyzed in order to determine phylogeny.
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[Australian National Univ.] A program for calculating and displaying compatibility matrices as an aid in determining reticulate evolution in molecular sequences.
[Univ. of Oxford, Department of Zoology] A program that will simulate the evolution of nucleotide sequences along a phylogeny, using common models of the substitution process.
[Jody Hey] A computer program for the analysis of comparative DNA sequence data, and is primarily intended for data sets with multiple closely related sequences.
[Impkin Inc.] A program designed to read a data file comprising aligned character arrays (such as DNA sequence data) or distance data in the form of a matrix, and perform some simple spectral analysis procedures on that data.
[University of Bielefeld] An interactive program for analyzing and visualizing evolutionary data. Based on the split decomposition method, this program takes input as a distance matrix, or a set of aligned sequences, and produces output as a graph that represents the evolutionary relationships between taxa.
[University of Antwerp (UIA) ] (Yves Van de Peer ) “TREECON is a software package developed primarily for the construction and drawing of phylogenetic trees on the basis of evolutionary distances inferred from nucleic and amino acid sequences.”
[Univ. of Sydney] Hasegawa test with any level of significance.
[Univ. of Glasgow, Taxonomy & Systematics] TreeMap is a program for comparing host and parasite trees.
[Univ. of Glasgow, Taxonomy & Systematics] A simple program for displaying phylogenies that reads standard NEXUS and PHYLIP formatted trees.
[Univ. of Oxford] A program that will simulate the evolution of DNA sequences under a coalescent model, which allows exponential population growth, population subdivision according to an island model, migration, and recombination.
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