title: pHMM-tree: phylogeny of profile hidden Markov models.
abstract: Protein families are often represented by profile hidden Markov models (pHMMs). Homology between two distant protein families can be determined by comparing the pHMMs. Here we explored the idea of building a phylogeny of protein families using the distance matrix of their pHMMs. We developed a new software and web server (pHMM-tree) to allow four major types of inputs: (i) multiple pHMM files, (ii) multiple aligned protein sequence files, (iii) mixture of pHMM and aligned sequence files and (iv) unaligned protein sequences in a single file. The output will be a pHMM phylogeny of different protein families delineating their relationships. We have applied pHMM-tree to build phylogenies for CAZyme (carbohydrate active enzyme) classes and Pfam clans, which attested its usefulness in the phylogenetic representation of the evolutionary relationship among distant protein families.
  
  
  
  This software is implemented in C/C ++ and is available at http://cys.bios.niu.edu/pHMM-Tree/source/.
  
  
  
  zhanghan@nankai.edu.cn or yyin@niu.edu.
  
  
  
  Supplementary data are available at Bioinformatics online.
authors.affiliation: College of Computer and Control Engineering, Nankai University, Tianjin, China.
authors.forename: Luyang
authors.initials: L
authors.lastname: Huo
authors.affiliation: College of Computer and Control Engineering, Nankai University, Tianjin, China.
authors.forename: Han
authors.initials: H
authors.lastname: Zhang
authors.affiliation: College of Computer and Control Engineering, Nankai University, Tianjin, China.
authors.forename: Xueting
authors.initials: X
authors.lastname: Huo
authors.affiliation: Department of Biological Sciences, Northern Illinois University, DeKalb, IL, USA.
authors.forename: Yasong
authors.initials: Y
authors.lastname: Yang
authors.affiliation: Department of Biological Sciences, Northern Illinois University, DeKalb, IL, USA.
authors.forename: Xueqiong
authors.initials: X
authors.lastname: Li
authors.affiliation: Department of Biological Sciences, Northern Illinois University, DeKalb, IL, USA.
authors.forename: Yanbin
authors.initials: Y
authors.lastname: Yin
mesh_terms: D000465:Algorithms; D008390:Markov Chains; D010802:Phylogeny; D011506:Proteins / Q000145:classification*; D016415:Sequence Alignment; D020539:Sequence Analysis, Protein; D012984:Software
chemical_list: D011506:Proteins