TreeBest specifications


Unique identifier OMICS_14581
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 citations

PMCID: 5026255

[…] 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: 2699529

[…] 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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