Overview

Problem

• Given a free gene tree, find where to place the root such that duplications and losses are minimized. Duplications are prioritized before losses.

• Given a rooted gene tree, map the gene tree onto the species tree.

• Removing in-paralogous.

Depending on the model and assumptions this can be solved in many ways.

Solution

Softparsmap is based on the model presented in [1] which is using duplications, losses, and alleles to explain the deviation found between the species tree and the gene tree. Softparsmap assumes that species events that is close enough in time such that alleles might survive, is presented in the species tree as uncertainties. Furthermore, genes can only be transfered from one species to another through a speciation event.

With some additional Java programming the package can be adapted to almost any source of data. However, existing interface retrieve species trees from NCBI Taxonomy, sequence data from an XML file, the gene trees from one file per family, and the results are written to one or two files per family.

Current available features are

• rooting free gene trees by minimizing duplications and losses while allowing weak edges to be collapsed

• removing in-paralogous while rooting the gene tree or just before the result is saved

• resolve uncertainties by inserting splits from the species tree and using out-groups

• mapping rooted gene trees onto the species trees

• comparing gene trees using splits

• supports the Newick and the Schreiber format for parsing in and out trees

• the package is divided into parts that can be replaced to meet specific needs