RANGER-DTLx (prototype implementation)
RANGER-DTLx is an extended version of the Ranger-DTL program from the RANGER-DTL 2.0 software package and can be used for inferring gene family evolution by speciation, gene duplication, horizontal gene transfer, and gene loss. The prototype implementation of RANGER-DTLx available here takes as input a rooted gene tree and a rooted species tree and reconciles the two by postulating speciation, duplication, transfer, and loss events. The distinguishing feature of RANGER-DTLx is that it implements an extended version of the Duplication-Transfer-Loss (DTL) reconciliation model, called the DTLx reconciliation model, that can account for horizontal gene transfer events from unsampled or extinct species lineages. Further details on the DTLx reconciliation model appear in the manuscript cited below.
RANGER-DTLx is written in C++ and is built on top of base code from the RANGER-DTL 2.0 software package. RANGER-DTLx was implemented by Samson Weiner and is available open source under GNU GPL. Complete source code, a pre-compiled Linux executable, and a user manual are available below.
- Software download: Source code, Pre-compiled Linux executables (64 bit)
- User manual: RANGER-DTLx_Manual.pdf
The biological and simulated datasets used in this research are also available below.
- Biological dataset: DTLx_biological.zip
- Simulated dataset: DTLx_simulated.zip
This software can be cited as follows:
- Improved Duplication-Transfer-Loss Reconciliation with Extinct and Unsampled Lineages
Samson Weiner, Mukul S. Bansal
Algorithms, 14(8): 231, 2021.
Funding: Development of the software resource(s) available from this webpage was funded in part by U.S. National Science Foundation awards MCB 1616514 and IES 1615573.
Contact: Please feel free to contact Mukul Bansal (mukul.bansal@uconn.edu) if you have any questions, concerns, or suggestions.