DupLoss-2: Species tree inference under gene duplication and loss
DupLoss-2 is a program for phylogenomic species tree inference using gene tree parsimony. It takes as input a collection of gene trees and seeks a species tree that best reconciles the input gene trees under a gene duplication and loss reconciliation model. DupLoss-2 can lead to significant improvements in species tree reconstruction accuracy compared to other existing methods on phylogenomic datasets where gene duplication and loss are the primary drivers of gene family evolution. DupLoss-2 is scalable to whole-genome datasets with thousands of gene trees from hundreds of taxa. Further methodological details and experimental results appear in the paper cited below.
DupLoss-2 is written in C++ and was implemented by Mukul Bansal. It is based on open-source code from the DupTree software package, originally written by Andre Wehe and Mukul Bansal. DupLoss-2 is available open source under GNU GPL from the GitHub link posted below. For convenience, standalone precompiled executables for Mac and Linux operating systems are also available below.
- User manual: DupLoss-2_UserManual.pdf
- Standalone precompiled executables: DupLoss-2 for macOS, DupLoss-2 for Linux
- Source code: https://github.com/Bansal-CompBioLab/DupLoss-2
This software can be cited as follows:
- DupLoss-2: Improved Phylogenomic Species Tree Inference under Gene Duplication and Loss
Rachel Parsons, Mukul S. Bansal
Under review
Funding: Development of the software resource(s) available from this webpage was funded in part by U.S. National Science Foundation award 15534211.
Contact: Please feel free to contact Mukul Bansal (mukul.bansal@uconn.edu) if you have any questions, concerns, or suggestions.