Category: Phylogenetic Analysis

Phylogen 1.1 – Simulate Phylogenies

Phylogen 1.1

:: DESCRIPTION

Phylogen implements some straight-forward birth-death models for simulating phylogenies. It is intended to be fast and flexible and can simulate very large trees (depending on memory and speed of computer). It will then optionally reconstruct trees only containing extant lineages or produce trees containing a random sample of lineages. Trees can be written to a file for analysis in other packages. It will also draw lineages-through-time-plots.

::DEVELOPER

Andrew Rambaut Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOS

:: DOWNLOAD

Phylogen

:: MORE INFORMATION

PI 2.0 – Test the Assumption of Phylogenetic Independence

PI 2.0

:: DESCRIPTION

PI ( Phylogenetic Independence) is a program  to conduct the Test For Serial Independence (TFSI) on continuously valued characters and the Runs Test on discretely valued characters (Abouheif 1999). The TFSI and Runs Test are used to test the assumption of phylogenetic independence within a set of comparative data, i.e., to test whether a trait is significantly associated with its phylogenetic history. This version of the program can perform the TFSI and Runs Test using either fully resolved phylogenetic trees or an unresolved trees (i.e. one with polytomies).

::DEVELOPER

Jeff Reeve and Ehab Abouheif

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux

:: DOWNLOAD

PI for win , for Linux

:: MORE INFORMATION

Citation:

Abouheif, E (1999)
A method for testing the assumption of phylogenetic independence in comparative data
Evolutionary Ecology Research 1: 895-909

covarionTest 20050610 – Covarion Structure Test

covarionTest 20050610

:: DESCRIPTION

covarionTest is a perl script that performs the heterogeneity or the covarion test.

::DEVELOPER

Cécile Ané

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOS
  • Perl

:: DOWNLOAD

covarionTest

:: MORE INFORMATION

Citation:

Cecile Ane, J. Gordon Burleigh, Michelle M. McMahon, Michael J. Sanderson.
Covarion structure in the plastid genome evolution: a new statistical test.
Mol. Biol Evol., 22(4):914-924. 2005

STC 1.2 – Reconstruct Large Phylogenies

STC 1.2

:: DESCRIPTION

STC (shortest triplet clustering algorithm) is a software to reconstruct phylogenies. The main idea is the introduction of a natural definition of so-called k-representative sets. Based on k-representative sets, shortest triplets are reconstructed and serve as building blocks for the STC algorithm to agglomerate sequences for tree reconstruction in O(n2) time for n sequences.

::DEVELOPER

Center of Integrative Bioinformatics Vienna (CIBIV)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOS

:: DOWNLOAD

STC

:: MORE INFORMATION

Citation

Le Sy Vinh and Arndt von Haeseler,
Shortest Triplet Clustering: Reconstructing Large Phylogenies,
BMC-Bioinformatics.6:92. 2005.

ProfDistS 0.9.9 beta – Construction of Large Phylogenetic Trees

ProfDistS 0.9.9 beta

:: DESCRIPTION

ProfDist is a user-friendly software package using the profile-neighbor-joining method (PNJ) in inferring phylogenies based on profile distances on DNA or RNA sequences. It is a tool for reconstructing and visualizing large phylogenetic trees providing new and standard features with a special focus on time efficency, robustness and accuracy.

::DEVELOPER

Matthias Wolf, Benjamin Ruderisch, Thomas Dandekar, Jörg Schultz, and Tobias Müller Department of Bioinformatics, University Würzburg

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOS

:: DOWNLOAD

ProfDistS

:: MORE INFORMATION

Citation

Friedrich J, Dandekar T, Wolf M and Müller T (2005):
ProfDist: A tool for the construction of large phylogenetic trees based on profile distances.
Bioinformatics 21: 2108-2109

FSTAT 2.9.3.2 – Estimate & Test Gene Diversities

FSTAT 2.9.3.2

:: DESCRIPTION

FSTAT is a computer package for PCs which estimates and tests gene diversities and differentiation statistics from codominant genetic markers. It computes both Nei and Weir & Cockerham families of estimators of gene diversities and F-statistics, and tests them using randomisation methods.

::DEVELOPER

Jérôme Goudet.

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

FSTAT

:: MORE INFORMATION

T-REX 4.01 – Reconstruct Phylogenetic Trees and Reticulation Networks

T-REX 4.01

:: DESCRIPTION

T-REX (tree and reticulogram reconstruction) is an application to reconstruct phylogenetic trees and reticulation networks from distance matrices. The application includes a number of tree fitting methods like NJ, UNJ or ADDTREE which have been very popular in phylogenetic analysis. At the same time, the software comprises several new methods of phylogenetic analysis such as: tree reconstruction using weights, tree inference from incomplete distance matrices or modeling a reticulation network for a collection of objects or species. T-REX also allows the user to visualize obtained tree or network structures using Hierarchical, Radial or Axial types of tree drawing and manipulate them interactively.

T-REX Online Version

::DEVELOPER

Vladimir Makarenkov

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOSX

:: DOWNLOAD

T-REX

:: MORE INFORMATION

Citation

Makarenkov, V. 2001.
T-Rex: Reconstructing and visualizing phylogenetic trees and reticulation networks,
Bioinformatics 17, 664-668.

GEODIS 2.6 – Nested Clade Phylogeographic Analysis

GEODIS 2.6

:: DESCRIPTION

GEODIS is a program for the calculation of the statistics and associated P-values for the nested clade analysis (NCA) developed by Templeton and collaborators. In the NCA, population structure can be separated from population history when it is assessed through rigorous and objective statistical tests using the temporal information contained in the a genealogy.

::DEVELOPER

David Posada’s Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Java

:: DOWNLOAD

GEODIS

:: MORE INFORMATION

Citation

Posada D, Crandall KA and Templeton AR. 2000.
GeoDis: A program for the Cladistic Nested Analysis of the Geographical Distribution of Genetic Haplotypes.
Molecular Ecology 9(4):487-488.

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.

TreeViewJ 1.1.2 – View & Analyze Phylogenetic Trees

TreeViewJ 1.1.2

:: DESCRIPTION

TreeViewJ is an open source, cross-platform tool for viewing and analyzing phylogenetic trees.  It provides the user with the capability to rename, color, and adjust the width of nodes and branches to produce publication-quality images.  If dates are available for taxa, the software can map them onto a timeline, and sort the tree in ascending or descending date order.

::DEVELOPER

Matthew W Peterson and Marc E Colosimo

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Java

:: DOWNLOAD

TreeViewJ

:: MORE INFORMATION

Citation

Peterson, M.W. and M.E. Colosimo,
TreeViewJ: an application for viewing and analyzing phylogenetic trees.
Source Code Biol Med, 2007. 2(1): p. 7.