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Builds, manipulates and displays phylogenetic trees. TreeBest is particularly designed for building gene trees with a known species tree and is highly efficient and accurate. It is previously known as NJTREE and has been largely used in the TreeFam database, Ensembl Compara and OPTIC database. Several methods were developed to incorporate species phylogenies in building gene trees. These methods greatly improve the accuracy of gene trees, without adding too much computational overhead.

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TreeBest classification

TreeBest specifications

Software type:
Package/Module
Restrictions to use:
None
Input format:
JSON
Programming languages:
Java
Computer skills:
Advanced
Stability:
Beta
Maintained:
Yes
Interface:
Command line interface, Graphical user interface
Input data:
Coding sequences (CDS) to protein sequences, a species tree, gene feature information in JSON format
Operating system:
Unix/Linux, Mac OS, Windows
License:
GNU General Public License version 2.0
Version:
1.9.2
Requirements:
FLTK
Source code URL:
https://sourceforge.net/p/treesoft/code/HEAD/tree/
Conda:
https://bioconda.github.io/recipes/treebest/README.html

TreeBest support

Documentation

Maintainer

  • Heng Li <>

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