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TreeTime specifications


Unique identifier OMICS_14804
Name TreeTime
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Input data Multi-locus sequence data
Input format Nexus
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Numpy, Scipy, BioPython, Pandas
Maintained Yes



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  • person_outline Dirk Metzler <>

Publications for TreeTime

TreeTime in publications

PMCID: 5923486
PMID: 29652800
DOI: 10.3390/v10040192

[…] iterations by majority-rule tree based criteria and general time reversible substitution model with gamma distribution and invariant sites (gtr + g + i). molecular-clock phylogeny was inferred using treetime 0.94 []. the tree was visualized and colour-coded in figtree v1.4.3 (available at, since whole genome sequences of sat genotypes […]

PMCID: 5790871
PMID: 29404424
DOI: 10.1128/mSystems.00108-17

[…] and susceptible isolates for each drug using vcflib v1.0.0-rc0-262-g50a3 ( for nonbiallelic snps, we calculated fst for the two most common variants., we used treetime () to perform ancestral reconstruction and place snps and indels in the phylogeny. we identified homoplastic snps and indels as those arising multiple times in the phylogeny., unless […]

PMCID: 5705806
PMID: 29202045
DOI: 10.1128/mSphere.00511-17

[…] u for each category of sites. to reduce the impact of lateral gene transfer on the sfs, we removed sites where the origin was outside lineage u based on results of fastgear analysis., we used treetime () to reconstruct the evolutionary history of the variant in aas using the maximum likelihood phylogeny inferred using raxml., we performed demographic inference with the synonymous sfs […]

PMCID: 3044269
PMID: 21342544
DOI: 10.1186/1471-2105-12-S1-S15

[…] database [], specifically accession tf105503 (ring-box protein 1) from treefam 7.0. we used a species tree generated from treefam, with the branch lengths obtained from diversification dates in the treetime database []. to root the gene trees, we first identified all most parsimonious rootings (the rootings that minimize the number of duplications) using urec []. all parsimony rootings […]

PMCID: 2719621
PMID: 19570207
DOI: 10.1186/1471-2148-9-151

[…] an old world family of lizards with a poor fossil record and uncertain phylogeny. four different models of rate variation are tested in a new program for bayesian phylogenetic analysis called treetime, based on a combination of mitochondrial and nuclear gene sequences. we incorporate paleontological uncertainty into divergence estimates by expressing multiple calibration dates as a range […]

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TreeTime institution(s)
Biozentrum, University of Basel, Basel, Switzerland; SIB Swiss Institute of Bioinformatics, Basel, Switzerland

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