TreeFix specifications

Unique identifier:
OMICS_13201
Interface:
Command line interface
Input data:
TreeFix takes as input a gene tree, a multiple alignment, a species tree, a test statistic and significance level for likelihood equivalence.
Operating system:
Unix/Linux, Mac OS, Windows
Computer skills:
Advanced
Stability:
Stable
Maintained:
Yes
Software type:
Framework/Library
Restrictions to use:
None
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.
Programming languages:
Python
Version:
1.1.1.10
Requirements:
C compiler, SWIG, Numpy, Scipy

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TreeFix distribution

download

TreeFix support

Documentation

Maintainer

  • Manolis Kellis <>

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Publications

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

Funding source(s)

This work was supported by a Kambourides Fellowship and National Science Foundation CAREER award [0644282].

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