Willows 1.1 – Tree and Forest Construction package

Willows 1.1

:: DESCRIPTION

Willows is a software package that includes three classifiers: classification tree, random forest, and deterministic forest. This package is built on RTREE mainly to implement the most efficient memory use for SNP data.

::DEVELOPER

The Collaborative Center for Statistics in Science(C2S2)

:: SCREENSHOTS

:: REQUIREMENTS

Windows / Linux /MacOsX
Java

:: DOWNLOAD

Willows

:: MORE INFORMATION

Citation:

Willows: a memory efficient tree and forest construction package.
Zhang H, Wang M, Chen X.
BMC Bioinformatics. 2009 May 5;10:130.

STREE – Survival Analysis Trees

STREE

:: DESCRIPTION

STREE represents one of the most popular uses of tree-based methods. This program identifies prognostic factors that are predictive of survival outcome and time to an event of interest. It partitions a study sample into strata to reveal distinct patt erns of survival among subgroups.

::DEVELOPER

The Collaborative Center for Statistics in Science(C2S2)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Linux /MacOsX

:: DOWNLOAD

STREE

:: MORE INFORMATION

TreeScan 1.0 – Genotype-phenotype Associations from Haplotype Trees

TreeScan 1.0

:: DESCRIPTION

TREESCAN is intended to provide p-values for the hypothesis of association between evolutionary clades and continuous traits, using haplotype trees.

::DEVELOPER

Phylogenomics Group at the University of Vigo

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / MacOsX / Linux

:: DOWNLOAD

TreeScan

:: MORE INFORMATION

Citation:

Posada D, Maxwell TJ, Templeton AR.
TreeScan: a bioinformatic application to search for genotype/phenotype associations using haplotype trees.
Bioinformatics 2005 21 (9): 2130-2132.doi: 10.1093/bioinformatics/bti29

TreeJuxtaposer 2.1 – View a Single Tree, or Compare Two or more Trees

TreeJuxtaposer 2.1

:: DESCRIPTION

TreeJuxtaposer lets you interactively view a single tree, or compare two or more trees. The software handles all kinds of trees, including phylogenetic trees, taxonomic trees, consensus trees, dendrograms from cluster hierarchies, and others. Uses nested parentheses (Newick/New Hampshire) data format. Guaranteed visibility of marked regions provides visual landmarks. Structural differences are automatically marked, and the marked clades highlight corresponding nodes on the trees through the use of a generalization of the Robinson-Foulds distance metric. Responsive drawing for even very large trees with advanced graphics techniques.

::DEVELOPER

TreeJuxtaposer Team

:: SCREENSHOTS

:: REQUIREMENTS

Windows / Linux / MacOSX
Java

:: DOWNLOAD

TreeJuxtaposer

:: MORE INFORMATION

Citation:

Tamara Munzner, Francois Guimbretiere, Serdar Tasiran, Li Zhang, and Yunhong Zhou.
TreeJuxtaposer: Scalable Tree Comparison using Focus+Context with Guaranteed Visibility
Proc. SIGGRAPH 2003, published as ACM Transactions on Graphics 22(3), pages 453–462

TreeStat 1.2 – Calculate Summary Statistics of a set of Trees

TreeStat 1.2

:: DESCRIPTION

TreeStat is an application that can process a set of trees in a PHYLIP or NEXUS format tree file and calculate a number of summary statistics for each. These are saved in a tab-delimited file for analysis in Tracer or statistics packages.

::DEVELOPER

Andrew Rambaut Group

:: SCREENSHOTS

:: REQUIREMENTS

Windows / Linux / MacOS
Java

:: DOWNLOAD

TreeStat

:: MORE INFORMATION

GeneTree 1.3 – Compare Gene and Species Trees

GeneTree 1.3

:: DESCRIPTION

GeneTree is an experimental program for comparing gene and species trees. The program can compute the cost of embedding a gene tree within a species tree, visually display the location and number of gene duplications and losses, and search for optimal species trees.

::DEVELOPER

Professor Rod Page

:: SCREENSHOTS

:: REQUIREMENTS

Windows / PowerMac

:: DOWNLOAD

GeneTree for win , for Power Macintosh

:: MORE INFORMATION

Citation

R D Page
GeneTree: comparing gene and species phylogenies using reconciled trees.
Bioinformatics. 1998;14(9):819-20.