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
C compiler, SWIG, Numpy, Scipy
Maintained Yes



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  • person_outline Manolis Kellis <>

Publication for TreeFix

TreeFix in publications

PMCID: 5941490
PMID: 29739321
DOI: 10.1186/s12864-018-4711-0

[…] groups with all five taxa present from the codon alignments using raxml [] with the gtr + γ nucleotide substitution model. we attempted to improve the accuracy of the gene tree topologies using treefix []. treefix uses the species tree, the ml estimate of the gene tree, and the multiple sequence alignment as input, and it searches for the rooted gene tree topology that implies the fewest […]

PMCID: 5910433
PMID: 29679020
DOI: 10.1038/s41598-018-24686-4

[…] each protein cluster as above, and inferred ml gene trees in raxml 8.1.3 under the wag model with gamma-distributed rate heterogeneity. gene trees were then reconciled with the species tree by treefix v1.1.10 using 100 iterations and raxml as the tree inference algorithm and the default duplication/loss cost model. we then identified protein orthogroups within reconciled gene trees using […]

PMCID: 5405339
PMID: 28444194
DOI: 10.1093/gbe/evx056

[…] the entire protein lengths with raxml v8.1.12 () using the lg4x model (). eight tree searches were performed to identify the ml tree. then we attempted to improve the ml gene tree topologies using treefix (), which takes the ml gene tree topology, the sequence alignment, and a species tree topology () and tries to find an alternate gene tree topology that implies fewer duplications and losses […]

PMCID: 5400391
PMID: 28087775
DOI: 10.1093/molbev/msw285

[…] (see part 2 of readme at github site)., in some cases, our pipeline led to large gene families with one or more duplications at the base of diptera. to both increase the computational efficiency of treefix (see below), and improve the accuracy of our rate estimation, we used a custom perl script ( on github) to split trees where the deepest node was inferred to be a duplication […]

PMCID: 5006594
PMID: 27577050
DOI: 10.1186/s12864-016-3034-2

[…] cryptogramma specified as the outgroup. because of the potential for short read lengths to limit the power of likelihood reconstructions, we assessed trees using a test of topology in the program treefix version 1.1.10 (likelihood model = treefix.models.raxmlmodel.raxmlmodel0.2.4; reconciliation model = treefix.models.duplossmodel.duplossmodel1.0.1) []. treefix optimizes gene tree topologies […]

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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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