MulRF is a platform-independent software program designed to infer species trees from incongruent multi-copy gene trees using a generalization of the Robinson-Foulds (RF) distance to multi-labeled trees. MulRF version 1.2 has the following additional features:

• Weighted input gene trees for species tree search.
• Topological constraints on the inferred species tree.
• Automated execution of multiple replicates of tree search heuristic.
• MulRF distance of a given species tree from gene trees.
• Visualization of input/output trees.

MulRF's source code is available at https://github.com/ruchiherself/MulRFRepo.
Check out this screenshot of MulRF in execution: 

Download MulRF (version 1.2)

MulRF1.2.zip

Manual

Available here.

Note: if you want to build species trees for multiple gene trees files in batch, then use command line executable MulRFSupertreeWin.exe, MulRFSupertreeLin, or MulRFSupertreeMac for Windows, Linus, or Mac, respectively, available in executables folder inside MulRF1.2.

Citations

If you use MulRF for research, please cite

• MulRF: a software package for phylogenetic analysis using multi-copy gene trees
  Ruchi Chaudhary, David Fernández-Baca, and J. Gordon Burleigh, Bioinformatics, doi:10.1093/bioinformatics/btu648.
   
• 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.
   

†This work was supported by NSF grants DEB-1208428 and CCF-1017189.

Older version of MulRF can be found here.

Contact Ruchi Chaudhary (ruchic@ufl.edu) if you have questions or suggestions.

< Page last updated: 25 February 2021 >