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A software package for high-performance phylogenetic profile searches on desktop computers. The package implements partial phylogenetic profiling (PPP) and double partial phylogenetic profiling (DPP), algorithms to facilitate protein family construction using phylogenetic profiles. The computational advances represented by the PPP and DPPP algorithms have the potential to take phylogenetic profiling beyond the limited correlation of pre-formed protein families, and to remove much of the insensitivity of previous methods due to the vagaries of protein cluster calculations. With ProPhylo, users are able to generate and modify custom profiles, iterate and refine hypotheses, and tune parameters to perform real-time profiling research in a manner distinctly more powerful than is currently available.

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ProPhylo classification

ProPhylo specifications

Software type:
Restrictions to use:
Operating system:
Unix/Linux, Mac OS, Windows
Computer skills:
Command line interface
Input data:
ProPhylo requires two databases: the cross-genome all vs. all BLAST search results (or a slice of this data set for at least one target genome), and the NCBI taxonomy database.
Programming languages:

ProPhylo distribution


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ProPhylo support


  • Daniel H. Haft <>


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J Craig Venter Institute, Chinakville, MD, USA

Funding source(s)

This work was supported by NIH grant R01 HGO04881.

Link to literature

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