TreeTime statistics

Tool stats & trends

Looking to identify usage trends or leading experts?

Protocols

TreeTime specifications

Information


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
Requirements
Numpy, Scipy, BioPython, Pandas
Maintained Yes

Download


download.png
github.png
conda.png

Versioning


No version available

Documentation


Maintainer


  • person_outline Dirk Metzler

Publications for TreeTime

TreeTime citations

 (5)
call_split

Full Genome Sequencing Reveals New Southern African Territories Genotypes Bringing Us Closer to Understanding True Variability of Foot and Mouth Disease Virus in Africa

2018
Viruses
PMCID: 5923486
PMID: 29652800
DOI: 10.3390/v10040192
call_split See protocol

[…] 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 http://tree.bio.ed.ac.uk/software/figtree/). […]

library_books

Signatures of Selection at Drug Resistance Loci in Mycobacterium tuberculosis

2018
mSystems
PMCID: 5790871
PMID: 29404424
DOI: 10.1128/mSystems.00108-17

[…] 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. […]

library_books

TreeTime: Maximum likelihood phylodynamic analysis

2018
Virus Evol
PMCID: 5758920
PMID: 29340210
DOI: 10.1093/ve/vex042

[…] and uses the packages numpy and scipy for optimization, linear algebra, and interpolation ) and . Computationally costly operations are cast into array operations executed by numpy whenever possible.TreeTime is organized as a hierarchy of classes. TreeAnc performs maximum-likelihood inference of ancestral sequences, ClockTree infers a time scaled phylogeny given a tree topology, and TreeTime adds […]

library_books

Adaptation in a Fibronectin Binding Autolysin of Staphylococcus saprophyticus

2017
PMCID: 5705806
PMID: 29202045
DOI: 10.1128/mSphere.00511-17

[…] We used TreeTime () to reconstruct the evolutionary history of the variant in aas using the maximum likelihood phylogeny inferred using RAxML. […]

call_split

Integration of Bayesian molecular clock methods and fossil based soft bounds reveals early Cenozoic origin of African lacertid lizards

2009
BMC Evol Biol
PMCID: 2719621
PMID: 19570207
DOI: 10.1186/1471-2148-9-151
call_split See protocol

[…] rallel chains we used a heating coefficient of 0.3. This resulted in a sample of size of 100 from the posterior distribution, taken from the cold chain.MCMC calculations were performed in the program TreeTime, freely available at []. Within that program, the following models were implemented:MC: Strict molecular clock model [], assumes a fixed rate of evolution along all branches of the tree.CPP: […]

Citations

Looking to check out a full list of citations?

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

TreeTime reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review TreeTime