MulRF (Old version)
ManualThe manual is available here.
Note: If you are planning to execute MulRF on ultra large data sets (e.g., data sets of several thousands of taxa), run MulRF with --initialtree option to obtain initial supertree. Additionally, use the below verions and output each kth supertree during the heuristic search using -k option instead of waiting for the execution to end. (Check help using -h.)
Simulated datasetsWe simulated gene trees over 50 and 100 taxa species trees. We used several parameter settings to generate four sets of gene trees: i) no duplications, losses, or LGT, ii) duplication and loss but no LGT, iii) LGT but no duplication and loss, and iv) duplication, loss, and LGT. See the paper (below) for full details.
Inferring Species Trees from Incongruent Multi-Copy Gene Trees Using the Robinson-Foulds Distance
Ruchi Chaudhary, J. Gordon Burleigh, and David Fernández-Baca, Algorithms for Molecular Biology 8:28, 2013.
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