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Most Parsimonious Reconciliation in the Presence of Gene Duplication, Loss, and Deep Coalescence.
Yi-Chieh Wu, Matthew D. Rasmussen, Mukul S. Bansal, and Manolis Kellis.
Genome Research. 2014. doi: 10.1101/gr.161968.113

Multiple Optimal Reconciliations under the Duplication-Loss-Coalescence Model.
Haoxing Du, Yi Sheng Ong, Marina Knittel, Ross Mawhorter, Nuo Liu, Gianluca Gross, Reiko Tojo, Ran Libeskind-Hadas, and Yi-Chieh Wu.
IEEE/ACM Transactions on Computational Biology and Bioinformatics. In press. doi: 10.1109/TCBB.2019.2922337

Inferring Pareto-Optimal Reconciliations across Multiple Event Costs under the Duplication-Loss-Coalescence Model.
Ross Mawhorter, Nuo Liu, Ran Libeskind-Hadas, and Yi-Chieh Wu.
BMC Bioinformatics. 2019. doi: 10.1186/s12859-019-3206-6

An Integer Linear Programming Solution for the Most Parsimonious Reconciliation Problem under the Duplication-Loss-Coalescence Model.
Morgan Carothers, Joseph Gardi, Gianluca Gross, Tatsuki Kuze, Nuo Liu, Fiona Plunkett, Julia Qian, Yi-Chieh Wu.

Address correspondence to: Yi-Chieh Wu (yjw AT cs DOT hmc DOT edu)
Equal contribution


DLCpar is a reconciliation method for inferring gene duplications, losses, and coalescence (accounting for incomplete lineage sorting).


Supplemental data

We evaluated DLCpar using the same datasets used to evaluate DLCoal. This included 5351 real gene families across the 16 fungal genomes, as well as simulated gene families across the 12 Drosophila and 15 primates (+ 2 outgroup species) clades. In addition, we evaluated DLCpar on simulated gene families with simulated species trees. (The species trees are the same as those used to evaluate TreeFix.) Additional simulated datasets available upon request.

Note that DLCpar uses many of the same conventions as other phylogenetic programs developed by our group (e.g. SPIMAP, TreeFix, DLCoal). If a file format or directory structure is unclear, you might be able to find more information at one of these websites.


Last updated 06/18/20.