- Executables for: Linux, Windows, Mac
- Manual: pdf
- Source code: Source Code (available open source under GNU GPL version 3)
- RANGER-DTL to RecPhyloXML converter: A Python script that can convert reconciliations from the output format used by RANGER-DTL to the newly developed RecPhyloXML format is available below.
RANGER-DTL 2.0 (short for Rapid ANalysis of Gene family Evolution using Reconciliation-DTL) is a software package for inferring gene family evolution by speciation, gene duplication, horizontal gene transfer, and gene loss. The software takes as input a gene tree (rooted or unrooted) and a rooted species tree and reconciles the two by postulating speciation, duplication, transfer, and loss events. RANGER-DTL 2.0 implements many new algorithms that vastly improve upon the capability and functionality of the previous version of RANGER-DTL (version 1, available from http://compbio.mit.edu/ranger-dtl/).
Some new capabilities of RANGER-DTL 2.0 include (i) principled handling of unrooted gene trees by considering all possible optimal rootings, instead of just a single arbitrarily chosen optimal rooting, (ii) uniformly random sampling of the space of all optimal reconciliations, making it possible to compute multiple optimal reconciliations and account for the variability in optimal reconciliation scenarios, (iii) handling gene tree uncertainty by collapsing weakly supported gene tree edges and computing and considering all optimal resolutions of the gene tree, and (iv) computing support values for individual DTL event inferences and species mapping assignments while accounting for multiple optimal reconciliations, alternative event cost assignments, alternative gene tree rootings, and topological uncertainty. RANGER-DTL 2.0 can efficiently analyze trees with many hundreds or even thousands of taxa, can handle both undated and dated species trees (i.e., both cladograms and chronograms), and allows for the use of distance-dependent transfer costs. Further details on the functionality of RANGER-DTL 2.0 appear in the manual. This software is available open source under GPL version 3.
RANGER-DTL 2.0 can be cited as follows:
- RANGER-DTL 2.0: Rigorous Reconstruction of Gene-Family Evolution by Duplication, Transfer, and Loss
Mukul S. Bansal, Manolis Kellis, Misagh Kordi, Soumya Kundu.
Bioinformatics, 34(18): 3214–3216, 2018.
The software implements algorithms described in the following publications:
- Efficient Algorithms for the Reconciliation Problem with Gene Duplication, Horizontal Transfer, and Loss
Mukul S. Bansal, Eric J. Alm, Manolis Kellis.
ISMB 2012; Bioinformatics, 28: i283-i291, 2012.
- Reconciliation Revisited: Handling Multiple Optima when Reconciling with Duplication, Transfer, and Loss
Mukul S. Bansal, Eric J. Alm, Manolis Kellis.
Journal of Computational Biology (JCB), 20(10): 738-754, 2013.
A preliminary version of this paper appeared in RECOMB 2013.
- Exact Algorithms for Duplication-Transfer-Loss Reconciliation with Non-Binary Gene Trees
Misagh Kordi and Mukul S. Bansal.
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), 16(4): 1077-1090, 2019.
A preliminary version of this paper appeared in ACM-BCB 2016.
- On the Impact of Uncertain Gene Tree Rooting on Duplication-Transfer-Loss Reconciliation
Soumya Kundu and Mukul S. Bansal.
BMC Bioinformatics, 19(Suppl 9):290, 2018
RANGER-DTL to RecPhyloXML converter
Individual (non-aggregated) reconciliation outputs from RANGER-DTL can be converted into the recently developed XML-based format for reconciliations, RecPhyloXML, by using the following Python script. This converter was implemented and tested by Taylor Wade and Zack Eisbach, with further support provided by Samson Weiner.
- RANGER-DTL to RecPhyloXML converter download: RANGER-DTL_RecPhyloXML.zip
RANGER-DTL-RT: A heuristic for DTRL reconciliation
A simple heuristic algorithm for estimating DTRL (Duplication, Additive Transfer, Replacing Transfer, Loss) reconciliations by classifying transfers inferred by RANGER-DTL as being either additive or replacing was proposed in the paper cited below. A prototype implementation of this heuristic for estimating optimal DTRL reconciliations is available here. This implementation first computes an optimal DTL reconciliation using RANGER-DTL and then uses a simple heuristic (described in the cited paper) to classify each inferred transfer event as being either a replacing transfer or an additive transfer. Input and output are identical to that of RANGER-DTL (except that transfers are labeled as additive or replacing), as are usage instructions. The simulated datasets used in the paper are also available below.
UPDATE: Note that even more accurate heuristics for estimating DTRL reconciliations have now been developed and are implemented in the ARTra software package available from https://compbio.engr.uconn.edu/software/ARTra/.
- Executables for: Linux, Mac, Windows
- Simulated datasets: These are the datasets used for experimentally evaluating the accuracy of the heuristic.
- Source code: Available open source under GPL version 3; please email Mukul Bansal (email@example.com) if you would like a copy of the source code.
The RANGER-DTL-RT software can be cited as follows:
- On Inferring Additive and Replacing Horizontal Gene Transfers Through Phylogenetic Reconciliation
Misagh Kordi, Soumya Kundu, Mukul S. Bansal.
ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB) 2019; Proceedings, pages 514-523.
Funding: Development of the software resource(s) available from this webpage was funded in part by U.S. National Science Foundation awards IIS 1553421, MCB 1616514, and IES 1615573.