POPE – Phylogeny, Ortholog and Paralog Extractor

POPE

:: DESCRIPTION

POPE is a tool to aid high-throughput phylogenetic analysis.POPE provides an integrated platform for automatic ortholog identification. Intermediate steps can be visualized, modified and analyzed in order to assess and improve the underlying quality of orthology and paralogy assignments.

::DEVELOPER

Thorhildur Juliusdottir

:: SCREENSHOTS

:: REQUIREMENTS

Linux / Windows / MacOsX
Java

:: DOWNLOAD

POPE

:: MORE INFORMATION

Citation:

Bioinformatics. 2008 Dec 1;24(23):2778-9. Epub 2008 Oct 10.
POPE–a tool to aid high-throughput phylogenetic analysis.
Juliusdottir T, Pettersson F, Copley RR.

Gene-warp 3.2 – Generate Alignment Matrices, Explore Temporal Asynchrony in Expression of Orthologs

Gene-warp 3.2

:: DESCRIPTION

Gene-warp is a tool to select ortholog pairs with best alignments and to explore alignment paths (not expression profiles!) shared by many genes. The program takes as an input two related datasets, containing profiles of orthologous genes.

::DEVELOPER

Dmitri Papatsenko

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows

:: DOWNLOAD

Gene-warp

:: MORE INFORMATION

Citation

Goltsev Y, Papatsenko D.
“Time warping of evolutionary distant temporal gene expression data based on noise suppression”
BMC Bioinformatics. 2009 Oct 26;10:353.