DLCpar
paper | download | supplemental data

Paper

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. In press. doi: 10.1101/gr.161968.113

Multiple Optimal Reconciliations with Gene Duplication, Loss, and Coalescence.
Haoxing Du, Yi Sheng Ong, and Yi-Chieh Wu.
In prep.

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

Download

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

Requirements

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.

References


Last updated 09/28/16.