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TreeBest specifications


Unique identifier OMICS_14581
Name TreeBest
Alternative name Tree Building guided by Species Tree
Software type Package/Module
Interface Command line interface, Graphical user interface
Restrictions to use None
Input data Coding sequences (CDS) to protein sequences, a species tree, gene feature information in JSON format
Input format JSON
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.9.2
Stability Beta
Maintained Yes




No version available



  • person_outline Heng Li

TreeBest 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

[…] en a gene tree and a species tree.Most integrative methods for gene tree reconstruction assume a simplified model of gene family evolution where gene gain events are reduced to gene duplication (e.g. TreeBeST [], TreeFix [], ProfileNJ [], NOTUNG [], SPIMAP [], Giga []). In fact, the MPR problem for the Duplication-Loss (hereafter denoted DL) model of gene family evolution is linear-time solvable [ […]


Enzootic situation and molecular epidemiology of Brucella in livestock from 2011 to 2015 in Qingyang, China

PMCID: 5882930
PMID: 29615607
DOI: 10.1038/s41426-018-0060-y

[…] oftware for rapid clustering of similar proteins with a threshold of 50% pairwise identity and 0.7 length difference cutoff. A phylogenetic tree was constructed from the orthologous gene sequences by TreeBeST using the neighbor-joining method, and the number of bootstrap samples was 1000,. […]


Genome Wide Analysis of Mycoplasma bovirhinis GS01 Reveals Potential Virulence Factors and Phylogenetic Relationships

PMCID: 5940136
PMID: 29602809
DOI: 10.1534/g3.118.200018

[…] n amino acid. Multiple sequences of single-copy core genes among 19 Mycoplasma strains were aligned using MUSCLE v3.8.31 (). Phylogenetic trees based on the single-copy core genes were constructed by TreeBeST v1.9.2 () using the maximum likelihood model with 1000 bootstrap replicates under default parameters and by MrBayes v.3.2.6 () using Bayesian inference method. Bayesian inference phylogenyeti […]


Adaptive Transcriptome Profiling of Subterranean Zokor, Myospalax baileyi, to High Altitude Stresses in Tibet

Sci Rep
PMCID: 5856782
PMID: 29549310
DOI: 10.1038/s41598-018-22483-7

[…] nscriptome sequencing was performed on animals from three altitudinally distinct populations of the Tibetan Plateau. Genetic divergence was estimated by the Neighbor-Joining (NJ) cluster method using TreeBeST v1.9.2, and by the principal component analysis (PCA) based on the SNPs across the transcriptome. The permutation test was conducted for PCA analysis to ecologically differentiate the H from […]


Genetic Diversity, Molecular Phylogeny, and Selection Evidence of Jinchuan Yak Revealed by Whole Genome Resequencing

PMCID: 5844314
PMID: 29339406
DOI: 10.1534/g3.118.300572

[…] n structure. To clarify the phylogenetic relationship from a genome-wide perspective, we constructed an individual-based neighbor-joining tree with 1000 bootstrap values based on p-distance using the TreeBest software ( We also conducted principal component analysis (PCA) to evaluate the genetic structure by utilizing the GCTA software (http://cnsgen […]


De novo assembly and characterization of the Hucho taimen transcriptome

Ecol Evol
PMCID: 5773338
PMID: 29375797
DOI: 10.1002/ece3.3735

[…] identities >70% and alignment coverage >50%. The protein sequences of paralog pairs were aligned with MUSCLE, and the protein alignments were back‐translated to coding sequence (CDS) alignments using TreeBest software. The CDS alignments were used to calculate the Ka/Ks values using the CodeML (pairwise mode) of PAML (Yang, ).Lastly, we performed a systematic cross‐species analysis between taimen […]


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