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TreefixDTL specifications


Unique identifier OMICS_31847
Name TreefixDTL
Alternative name Treefix-DTL
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data A single maximum likelihood (ML) gene tree.
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Version 1.0.2
Stability Stable
Numpy, Scipy
Maintained Yes




No version available


  • person_outline Mukul S. Bansal
  • person_outline Manolis Kellis

Additional information

Publication for TreefixDTL

TreefixDTL citations


GATC: a genetic algorithm for gene tree construction under the Duplication Transfer Loss model of evolution

BMC Genomics
PMCID: 5954287
PMID: 29764363
DOI: 10.1186/s12864-018-4455-x

[…] To measure the efficiency of GATC in reconstructing accurate gene trees, we compared its performance, on a simulated dataset, to four different gene tree reconstruction methods: ecceTERA [], TreeFix-DTL [], ProfileNJ [], MowgliNNI [] and RAxML []. In contrast to RAxML which is a sequence-only method, the former four methods use both sequences and species tree information. We also used GAT […]


Genome scale phylogenetic analysis finds extensive gene transfer among fungi

PMCID: 4571573
PMID: 26323765
DOI: 10.1098/rstb.2014.0335

[…] to be slow, which motivated other approaches based on the consideration of a set of candidate gene trees obtained using faster approaches that do not consider a species tree. These approaches include TreefixDTL [], ALE [,] and TERA []. The latter two approaches are extensions of an idea initially proposed in [] and formalized in [] and are particularly fast and accurate. They are based on the ‘ama […]


Improved gene tree error correction in the presence of horizontal gene transfer

PMCID: 4393519
PMID: 25481006
DOI: 10.1093/bioinformatics/btu806
call_split See protocol

[…] In our experimental study, we applied the methods RAxML (), NOTUNG (), TreeFix (), MowgliNNI (), AnGST () and our new method TreeFix-DTL, to simulated datasets and evaluated the accuracy of the inferred gene trees. RAxML is a well-known method used for reconstructing a ML tree from sequence data and represents the baseline […]


Joint amalgamation of most parsimonious reconciled gene trees

PMCID: 4380024
PMID: 25380957
DOI: 10.1093/bioinformatics/btu728
call_split See protocol

[…] e aware methods, including TERA, we used the DTL costs δ = 2, τ = 3, λ = 1 obtained by using a criteria based on minimizing the change in ancestral genome sizes on a large biological dataset. We ran TreeFix-DTL with default parameters, JTT/GTR with a gamma distribution as models of evolution, and as a starting tree the PhyML tree. MowgliNNI was run with default parameters, a threshold of 50 for w […]


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TreefixDTL institution(s)
Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Computer Science and Engineering, University of Connecticut, Storrs, CT, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Cambridge, MA, USA; Broad Institute, Cambridge, MA, USA
TreefixDTL funding source(s)
Supported by a National Science Foundation [CAREER award 0644282], National Institutes of Health [RC2 HG005639], National Science Foundation AToL [0936234], and startup funds from the University of Connecticut.

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