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University of Connecticut School of Engineering Computational Biology Laboratory

Software

  • RANGER-DTL: Short for Rapid ANalysis of Gene family Evolution using Reconciliation-DTL, this 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 implements the algorithms presented in the ISMB 2012, RECOMB 2013, and ACM-BCB 2016 papers listed on the publications page and makes it possible to perform rigorous evolutionary analyses of even large gene families with thousands of taxa while accounting for confounding factors such as gene tree uncertainty and multiple optima. It can be downloaded from http://compbio.engr.uconn.edu/software/RANGER-DTL/
     
  • TreeFix: This is a program for very accurate reconstruction of eukaryotic gene trees. TreeFix takes as input a maximum likelihood gene tree topology, a known species tree, and a multiple sequence alignment for the gene family and outputs a more accurate gene tree topology that has statistically equivalent sequence support and better agreement with the species tree topology. Further technical details and experimental evaluation appear in the Systematic Biology paper listed on the publications page. TreeFix was programmed by Yi-Chieh Wu and can be downloaded from http://compbio.mit.edu/treefix/.
     
  • TreeFix-DTL: This is a program for very accurate reconstruction of microbial gene trees (with horizontal gene transfer). Like Treefix above, TreeFix-DTL takes as input a maximum likelihood gene tree topology, a known species tree, and a multiple sequence alignment for the gene family and outputs a more accurate gene tree topology while accounting for horizontal gene transfer, gene duplication, and gene loss. Further technical details and experimental evaluation appear in the Bioinformatics paper listed on the publications page. TreeFix-DTL was programmed by Yi-Chieh Wu and can be downloaded from http://compbio.mit.edu/treefix-dtl/.
     
  • RF-Supertrees: This is a fast and accurate supertree program for rooted phylogenetic trees. It searches for a supertree that minimizes the total (rooted) Robinson-Foulds distance (i.e. symmetric difference) between the supertree and the input trees. RF-Supertrees implements efficient search algorithms described in the paper Robinson-Foulds Supertrees listed on the publications page, and can be downloaded from http://genome.cs.iastate.edu/CBL/RFsupertrees/.
     
  • DupTree: This is a tool box for constructing species phylogenies from genome-scale multi-locus data using gene tree parsimony. The idea is to find the species tree that best reconciles the input gene trees in terms of gene duplications. Joint programming work with Andre Wehe. This toolbox implements the fast local search algorithm described in the RECOMB'07 paper listed on the publications page. DupTree can be downloaded from http://genome.cs.iastate.edu/CBL/DupTree/.
     
  • DupLoss and DeepC: These programs extend on the program DupTree and allow the construction of species phylogenies, from genome-scale multi-locus data, under the duplication-loss and deep coalescence cost models respectively. They implement the fast local search algorithms described in the APBC'10 paper listed on the publications page and are now available as part of the software package iGTP which can be downloaded from http://genome.cs.iastate.edu/CBL/iGTP/.
     
  • HiDe: HiDe (short for Highway Detection) is a software package for inferring highways of horizontal gene transfer (representing large-scale horizontal transfer of genes) in the evolutionary history of a set of species. HiDe implements the highway detection method described in this 2013 paper listed on the publications page and was programmed by undergraduate summer student Guy Banay under my supervision. HiDe can be downloaded from http://acgt.cs.tau.ac.il/hide/.
     

Last updated on March 30, 2017