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University of Connecticut School of Engineering Computational Biology Laboratory

RANGER-DTL 2.0

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.

The software implements algorithms described in the following publications:
  1. 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.

  2. 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.
     
  3. Exact Algorithms for Duplication-Transfer-Loss Reconciliation with Non-Binary Gene Trees
       Misagh Kordi and Mukul S. Bansal.
       ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB) 2016; pages 297-306.
       http://dx.doi.org/10.1145/2975167.2975198

  4. On the Impact of Uncertain Gene Tree Rooting on Duplication-Transfer-Loss Reconciliation
        Soumya Kundu and Mukul S. Bansal.
        Under review.
     


Contact: Please feel free to contact Mukul Bansal (mukul.bansal@uconn.edu) if you have any questions, concerns, or suggestions.
Last updated on March 22, 2017