SDI R

Overview

SDI R is for inferring gene duplications on a gene tree and for rooting by duplication minimization. For more information see Zmasek and Eddy (2001). A simple algorithm to infer gene duplication and speciation events on a gene tree. Bioinformatics, 17, 821-828.

SDI R has been implemented in Java as part of the forester libraries.

Download

» forester.jar

Source code is available at [forester] at sourceforge.net

Usage

java -cp path\to\forester.jar org.forester.application.sdi_r <gene tree in phyloXML format> <species tree in phyloXML format> Options: -ml to root by minimizing the mapping cost L (and also the sum of duplications) -md to root by minimizing the sum of duplications -mh to root by minimizing tree height (can be used together with -ml or -md)

Example

Download a example species tree ("arthropoda_species_tree.xml") and a example gene tree ("sample_unrooted_gene_tree.xml").

Then, run SDI R with the following command line:

% java -cp path\to\forester.jar org.forester.application.sdi_r -md sample_unrooted_gene_tree.xml arthropoda_species_tree.xml

The important point to keep in mind is that there must be at least one sub-element of the 'taxonomy' element which allows to match the sequences in the gene tree with a taxonomy in the species tree. In this example this sub-element of the 'taxonomy' element is 'code'.

Contact

Christian M Zmasek
phylosoft -at- gmail -dot- com

Last updated 2010.03.01