Softparsmap - The Soft Parsimony Map

Introduction

As species and their genomes diverge during evolutionary history, the sets of genes and their sequences also diverge. Gene duplication has been proposed as a crucial source of evolutionary innovation in organisms, like Eukaryotes, with small effective population sizes (Ohno, 1970). With duplication, comes initial redundancy, followed by neofunctionalization, subfunctionalization, and most commonly pseudogenization (Lynch, 2001). This differential retention of duplicate genes can result in a different phylogenetic tree for individual gene families than for the species as a whole. When differential parsing of shared ancestral gene and nucleotide polymorphism is added to the picture as well as uncertainty in tree calculation methodologioes, the correlation between the evolutionary history of a gene and a species becomes murky.

In the development of a large scale database for understanding species evolution through the evolution of gene families (Liberles et al., 2001; Roth et al., 2005), it has been necessary to develop a soft parsimony based approach to map gene trees onto species trees.

Description

Softparsmap is a Java based package implementing the soft parsimony approach presented in [1]. 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 species trees
• comparing gene trees using splits
• the package is divided into parts that can be replaced to meet specific needs

With 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, and the gene trees from one file per family. In order to parse in and out trees the Newick and Schreiber format is supported.

Documentation

The Quick Start Guide (as pdf) will guide you through the configuration and usage of the package. For more information see the Manual (as pdf).

Download

Softparsmap contains source files, compiled files, as well as documentation. The package Jooc is also included.

Installation

Download and unzip the package. Folders and files found in the main directory are

• build.xml - is the Ant build file
• classes - contains the binary classes
• docs - contains the documentation
• example - contains the example used in the Quick Start Guide.
• lib - contains the jar-files of Softparsmap and Jooc.
• src - contains source files

The jar-files found in the lib directory must be made visible to Java. This is done either by pointing to them at the prompt or by adding them to the system variable CLASSPATH. More information on how to set the class path is found at Solaris or at Windows.

Requirements

Softparsmap is dependent on a configuration tool called Jooc. Both packages require J2SE 1.4.2 or later.

Contact

Feedback is most certainly welcome. Send your additions, comments, questions, and criticisms to david dot liberles at bccs dot uib dot no

References

[1]	A. C. Berglund, P. J. Steffansson, M. J. Betts, and D. A. Liberles, Optimal gene trees from sequences and species trees using a soft interpretation of parsimony , Journal of Molecular Evolution (2006).