ET-TDT – Evolutionary Tree-Transmission Disequilibrium Test

ET-TDT

:: DESCRIPTION

ET-TDT is a procedure to combine the benefits of measured haplotype analysis with TDT to find which haplotypes or groups of haplotypes, as defined in an evolutionary tree, are responsible for increased (or decreased) relative risk for a genetic condition.

::DEVELOPER

COMPUTATIONAL GENETICS LAB

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 ET-TDT

:: MORE INFORMATION

Citation:

Howard Seltman, Kathryn Roeder, and B. Devlin,
Transmission/Disequilibrium Test Meets Measured Haplotype Analysis: Family-Based Association Analysis Guided by Evolution of Haplotypes
Am. J. Hum. Genet., 68:1250-1263, 2001

Phylip 3.695 – Free Package of Programs for Inferring Phylogenies

Phylip 3.695

:: DESCRIPTION

PHYLIP (the PHYLogeny Inference Package) is a free package of programs for inferring phylogenies  (evolutionary trees). It is distributed as source code, documentation files, and a number of different types of executables.

::DEVELOPER

Phylip Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows /  Mac OsX / Linux

:: DOWNLOAD

Phylip

:: MORE INFORMATION

Citation

Felsenstein, J. 1989.
PHYLIP – Phylogeny Inference Package (Version 3.2).
Cladistics 5: 164-166.

TREECON 1.3b – Construction & Drawing of Evolutionary Trees

TREECON 1.3b

:: DESCRIPTION

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. The evolutionary distance is computed for all pairs of organisms (or sequences) and a phylogenetic tree is inferred by considering the relationship between these distance values. In pairwise distance methods, the dissimilarity (fraction of substitutions) is usually converted into evolutionary distance by correcting for multiple mutations. The most frequently used equations to convert dissimilarities into distances are implemented in TREECON. On the basis of these distances, a phylogenetic tree can be inferred. Different algorithms are available to construct a phylogenetic tree and a few of them are implemented in TREECON. Programs for rooting the unrooted evolutionary trees, for drawing the tree on the screen, and for saving the tree are also included, as well as several other tools. Starting from a simple ASCII text file, containing nucleic acid or amino acid sequences with gaps required for mutual alignment, one can produce publishable trees in a user-friendly and straightforward way.

::DEVELOPER

Yves Van de Peer

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

TREECON

:: MORE INFORMATION

Citation

Van de Peer, Y., De Wachter, Y. (1994)
TREECON for Windows: a software package for the construction and drawing of evolutionary trees for the Microsoft Windows environment.
Comput. Applic. Biosci. 10, 569-70.

COMPONENT 2.0 – Analysis of Evolutionary Trees

COMPONENT 2.0

:: DESCRIPTION

COMPONENT is a computer program for analysing evolutionary trees and is intended for use in studies of phylogeny, tree shape distribution, gene trees/species trees, host-parasite cospeciation, and biogeography.

::DEVELOPER

Professor Rod Page

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

COMPONENT ; Source Code

:: MORE INFORMATION

For a review of COMPONENT see Joe Slowinski’s review in Cladistics 9: 351-353 (1993).