Introduction

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.

Publications

  1. pHMM-tree: phylogeny of profile hidden Markov models.
    Cite this
    Huo L, Zhang H, Huo X, Yang Y, Li X, Yin Y, 2017-04-01 - Bioinformatics (Oxford, England)

Credits

  1. Luyang Huo
    Developer

    College of Computer and Control Engineering, Nankai University, China

  2. Han Zhang
    Developer

    College of Computer and Control Engineering, Nankai University, China

  3. Xueting Huo
    Developer

    College of Computer and Control Engineering, Nankai University, China

  4. Yasong Yang
    Developer

    Department of Biological Sciences, Northern Illinois University, United States of America

  5. Xueqiong Li
    Developer

    Department of Biological Sciences, Northern Illinois University, United States of America

  6. Yanbin Yin
    Investigator

    Department of Biological Sciences, Northern Illinois University, United States of America

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Summary
AccessionBT006612
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesC, C++
User InterfaceTerminal Command Line
Download Count0
Country/RegionUnited States of America
Submitted ByYanbin Yin