Softparsmap - Quick Start Guide


Table of Contents
Introduction
Quick Start
Input Format
Further Information

Introduction

Many of the methods for producing phylogenetic trees from sequence alignments, for example bayesian estimation (eg. MrBayes, Huelsenbeck and Ronquist 2001) and neighbor joining, produce free trees. Many of the analysis that we want to do on gene trees, for example ancestral sequence and Ka/Ks calculations (eg. TAED, Roth et al, 2005), require or are more understandable when applied to rooted trees. Softparsmap is a java package that uses 'soft parsimony' to root gene trees by mapping them on to a species tree [1].

Softparsmap outputs the rooting that minimizes the number of gene duplication and gene loss events. This parsimony is 'soft' because, prior to rooting, branches with support less than a user-defined threshold are changed so that they agree with the species tree. In-paralogous can be removed either prior to or after rooting, or both, with the most recent complete sequence kept.

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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).