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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).
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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.
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About us
Dr. Yanbin Yin's lab at Northern Illinois University
Dr. Han Zhang's lab at Nankai University