Phylogenetic Analysis

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Phylogenetic Analysis

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ANCML
[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.



[more info][11181]


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BIONJ
[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.




[more info][11182]


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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.


[more info][11183]


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CAIC
[Univ. of Oxford] This software implements a suite of phylogenetically comparative methods for data sets including continuous variables.


[more info][11184]


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Cluster
[Univ. of ALberta] A clustering program that uses single and complete linkage methods to determine the heirarchial clustering for a given data set.



[more info][11186]


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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.



[more info][11188]


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GeneTree
[R.D.M. Page, Univ. of Glasgow] A program for comparing gene and species trees.



[more info][11189]


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LVB 1.0
[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…




[more info][11190]


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MacClade
[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.


[more info][11191]


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MALIGN
[American Museum of Natural History] A program for the alignment of molecular sequences based on the most parsimonious tree that can be constructed by the program algorithm.




[more info][11192]



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PAML
[Ziheng Yang] A program package for phylogenetic analyses of DNA or protein sequences using maximum likelihood.



[more info][11193]


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Phylodendron
[Indiana University] This is an application for drawing phylogenetic trees.



[more info][11195]


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PHYLTEST
[Pennsylvania State Univ.] Allows a comparison of phylogenic trees, estimation of the pairwise distances, relative rate tests, and computation of the time of divergence.


[more info][11196]


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PLATO 2.11
[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.

[more info][11197]


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PSeq-Gen
[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.

[more info][11198]


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PUZZLE 3.1
[K. Strimmer and A. von Haeseler] This program reconstructs phylogenetic trees from molecular sequence data by maximum likelihood.




[more info][11199]


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QDate
[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.

[more info][11200]


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Quercus
[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.



[more info][11201]


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RAPDistance
[Armstrong, Gibbs, Peakall, Weiller] (Australian National University and the Bioinformatics Group) Records and fragment data can be analyzed in order to determine phylogeny.



[more info][11202]


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RASA 3.0
[Lyons-Weiler] This is software for relative apparent synapomorphy analysis.


[more info][11203]



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Reticulate
[Australian National Univ.] A program for calculating and displaying compatibility matrices as an aid in determining reticulate evolution in molecular sequences.



[more info][11204]


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Seg-Gen
[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.

[more info][11206]


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SITES
[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.




[more info][11207]


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Spectrum
[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.


[more info][11208]


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SplitsTRee2
[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.



[more info][11209]


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Treecon
[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.”



[more info][11210]


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TreeCons
[Univ. of Sydney] Hasegawa test with any level of significance.



[more info][11211]


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Treemap
[Univ. of Glasgow, Taxonomy & Systematics] TreeMap is a program for comparing host and parasite trees.



[more info][11212]


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Treeview
[Univ. of Glasgow, Taxonomy &amp Systematics] A simple program for displaying phylogenies that reads standard NEXUS and PHYLIP formatted trees.



[more info][11213]


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TREEVOLVE v1.32
[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.

[more info][11214]



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VORTEX
[Bob Lacy] This program is for population viability analysis.



[more info][11215]