TreeBest pipeline

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
Requirements FLTK
Maintained Yes



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  • person_outline Heng Li <>

TreeBest IN pipelines

PMCID: 5026255
PMID: 27401233
DOI: 10.1093/molbev/msw129

[…] the p-distance, with either one outgroup (i.e., o. a. musimon) or three outgroups (i.e., o. a. musimon, o. a. polii, and c. ibex), using the software treebest v1.9.2 (, last accessed august 6, 2013). a pca analysis was performed on an individual-scale for the 77 native sheep using the smartpca program in the package eigensoft v5.0 (patterson et al. […]

PMCID: 3575239
PMID: 23402223
DOI: 10.1186/1471-2164-14-95

[…] from blastp alignments, (2) pairwise orthologues are grouped into clusters, (3) sequences within a cluster are aligned using muscle [71], and (4) phylogenetic tree topologies are estimated using treebest [72] with clusters being split into orthologous groups using the pufferfish tetraodon as the outgroup., the completeness of these gene sets was examined in two ways. firstly, the number […]

PMCID: 3355756
PMID: 22645531
DOI: 10.3389/fpls.2011.00034

[…] used to infer duplication events and identify paralogous genes and orthologous genes. the current implementation of the analysis pipeline is based on muscle (edgar, 2004) to align sequences, and treebest (vilella et al., 2009), a maximum likelihood method. the tree reconciliation service uses a version of the ensembl compara database (vilella et al., 2009) that was extended to model […]

PMCID: 2699529
PMID: 19429695
DOI: 10.1093/nar/gkp295

[…] queries. the pipeline that uses tblastn is the focus of this article because it is more complex and may have wider application. target uses muscle (39) to calculate the multiple alignment and treebest (24) to generate the phylogenetic tree of the putative homologs with the neighbor-joining method (40). the other functions of target are carried out by several perl scripts developed […]

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