DLCpar is a phylogenetic program for inferring a most parsimonious reconciliation between a gene tree and species tree under a duplication-loss-coalescence model. DLCpar is a reconciliation package that maps a gene tree to a species tree by inferring gene duplications, losses, and coalescence (accounting for incomplete lineage sorting). DLCpar uses the labeled coalescent tree (LCT) to infer the species and locus to which a gene belongs.
More detail can be found at the project website, manual, and examples.
- Yi-Chieh Wu
- Morgan Carothers, Joseph Gardi, Gianluca Gross, Tatsuki Kuze, Nuo Liu, Fiona Plunkett, Julia Qian (ILP formulation)
- Ross Mawhorter and Nuo Liu (cost landscapes)
- Haoxing Du and Yi Sheng Ong (multiple optimal reconciliations)
- Matthew Rasmussen (compbio libraries)
If you use dlcpar, please cite
- Wu, Rasmussen, Bansal, Kellis.
Most Parsimonious Reconciliation in the Presence of Gene Duplication, Loss, and Deep Coalescence using Labeled Coalescent Trees.
Genome Research 24(3):475-486, 2014.
In addition, please cite the publication relevant to the method being used:
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Du, Ong, Knittel, Mawhorter, Liu, Gross, Tojo, Libeskind-Hadas, Wu.
Multiple Optimal Reconciliations under the Duplication-Loss-Coalescence Model.
IEEE/ACM Transactions on Computational Biology and Bioinformatics. In press.
This citation should be used if you count the number of optimal reconciliations or use uniform random sampling. -
Mawhorter, Liu, Libeskind-Hadas, Wu.
Infering Pareto-Optimal Reconciliations across Multiple Event Costs under the Duplication-Loss-Coalescence Model.
BMC Bioinformatics 20:639, 2019.
This citation should be used if you partition the landscape of event costs. -
Carothers, Gardi, Gross, Kuze, Liu, Plunkett, Qian, Wu.
An Integer Linear Programming Solution for the Most Parsimonious Reconciliation Problem under the Duplication-Loss-Coalescence Model.
Submitted.
This citation should be used if you solve using ILP.
Copyright (c) 2012-2019 by Yi-Chieh Wu, with modified Python libraries, original (C) 2005-2011 by Matthew Rasmussen.
DLCpar is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see https://www.gnu.org/licenses/.