RANGER-DTL 2.0: rigorous reconstruction of gene-family evolution by duplication, transfer and loss

Mukul S Bansal; Manolis Kellis; Misagh Kordi; Soumya Kundu

doi:10.1093/bioinformatics/bty314

RANGER-DTL 2.0: rigorous reconstruction of gene-family evolution by duplication, transfer and loss

Bioinformatics. 2018 Sep 15;34(18):3214-3216. doi: 10.1093/bioinformatics/bty314.

Authors

Mukul S Bansal¹, Manolis Kellis^{2

3}, Misagh Kordi¹, Soumya Kundu¹

Affiliations

¹ Department of Computer Science and Engineering, University of Connecticut, Storrs, CT, USA.
² Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA.
³ Broad Institute, Cambridge, MA, USA.

Abstract

Summary: RANGER-DTL 2.0 is a software program for inferring gene family evolution using Duplication-Transfer-Loss reconciliation. This new software is highly scalable and easy to use, and offers many new features not currently available in any other reconciliation program. RANGER-DTL 2.0 has a particular focus on reconciliation accuracy and can account for many sources of reconciliation uncertainty including uncertain gene tree rooting, gene tree topological uncertainty, multiple optimal reconciliations and alternative event cost assignments. RANGER-DTL 2.0 is open-source and written in C++ and Python.

Availability and implementation: Pre-compiled executables, source code (open-source under GNU GPL) and a detailed manual are freely available from http://compbio.engr.uconn.edu/software/RANGER-DTL/.

Supplementary information: Supplementary data are available at Bioinformatics online.

Publication types

Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Algorithms
Computational Biology / methods*
Evolution, Molecular*
Gene Duplication*
Software*