• What is pHMM-Tree?

    There are numerous softwares to build phylogenies of protein/DNA sequences. pHMM-Tree is the first software to generate a phylogeny of profile hidden markov models (HMMs). The algorithm behind pHMM-Tree is based on the profile-profile methods (Soding, 2005). It can be used to depict the evolutionary relationship of pHMMs (e.g. Pfam families of a clan or PANTHER subfamilies of a family).

  • How to run pHMM-Tree?

    pHMM-Tree was written in C/C++ language. It can flexibly handle four kinds of input: (1) multiple files each in pHMM format; (2) multiple files each with a multiple sequence alignment (MSA) in FASTA format; (3) mixture of 1 and 2; and (4) a file with unaligned protein sequences in FASTA format.

    Please cite Huo et al. Bioinformatics 2017 if you used our tool.