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A bioinformatics tool that integrates sequence data from two genetic markers into a single phylogenetic tree that can be used for diversity analyses. Our approach starts with a "foundation" phylogeny based on one genetic marker whose sequences can be aligned across organisms spanning divergent taxonomic groups (e.g., fungal families). Then, "extension" phylogenies are built for more closely related organisms (e.g., fungal species or strains) using a second more rapidly evolving genetic marker. These smaller phylogenies are then grafted onto the foundation tree by mapping taxonomic names such that each corresponding foundation-tree tip would branch into its new "extension tree" child.

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ghost-tree classification

ghost-tree specifications

Software type:
Restrictions to use:
Operating system:
Computer skills:
MUSCLE, FastTree, SUMACLUST, ghost-tree
Command line interface
Input data:
ghost-tree takes as input (1) the Foundation Alignment (for example, the Silva 18S alignment) where sequences are annotated with taxonomy; (2) the Extension Sequence Collection (for example, unaligned ITS sequences from the UNITE database); and (3) a taxonomy map, which contains taxonomic annotations of the sequences in (2).
BSD 3-clause “New” or “Revised” License

ghost-tree distribution


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ghost-tree support



  • Jennifer Fouquier <>


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Graduate Program in Bioinformatics and Medical Informatics, San Diego State University, San Diego, CA, USA; Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, USA; Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA; Institute for Systems Biology, Seattle, WA, USA; Department of Pediatrics, and Department of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA; Department of Biology, San Diego State University, San Diego, CA, USA; San Diego State University, San Diego, CA, USA

Funding source(s)

This work was supported in part by grants from the Alfred P. Sloan Foundation.

Link to literature

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