TreeFix specifications


Unique identifier OMICS_13201
Name TreeFix
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Input data TreeFix takes as input a gene tree, a multiple alignment, a species tree, a test statistic and significance level for likelihood equivalence.
Output data TreeFix outputs the optimal rooted gene tree (the gene tree with minimum cost and statistically equivalent likelihood). If multiple trees have minimum cost and are statistically equivalent, the one with minimum change in likelihood is returned.
Operating system Unix/Linux, Mac OS, Windows
Programming languages Python
Computer skills Advanced
Stability Stable
Requirements C compiler, SWIG, Numpy, Scipy
Maintained Yes



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  • person_outline Manolis Kellis <>

Publication for TreeFix

TreeFix institution(s)
Department of Electrical Engineering and Computer Science, Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY, USA; Broad Institute, Cambridge, MA, USA
TreeFix funding source(s)
This work was supported by a Kambourides Fellowship and National Science Foundation CAREER award [0644282].

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