ghost-tree is a bioinformatics tool that combines sequence data from two genetic marker databases into one phylogenetic tree that can be used for diversity analyses. One database is used as a backbone or scaffold because it provides better phylogeny across all phyla, and the other database provides finer taxonomic resolution.

ghost-tree requires two external software tools to build a hybrid-tree or the "ghost-tree":

MUSCLE (Version 3.8.31): http://www.drive5.com/muscle/downloads.htm

FastTree (Version >2.1.7): http://www.microbesonline.org/fasttree/#Install

To optionally (recommended) regroup the extension OTUs, ghost-tree requires SUMACLUST:

SUMACLUST (Version 1.0.01): http://metabarcoding.org/sumatra/wiki/download

Please install the software and make sure that it is in your PATH variable. To test this you should be able to type “muscle, fasttree or sumaclust” from command line and see the “usage” or “help” documentation for each software tool.

This project is currently under active development. If you're interested in contributing, please contact @JTFouquier.