ArticleBioinformatics (Oxford, England)2017
pHMM-tree: phylogeny of profile hidden Markov models.
Article in Bioinformatics (Oxford, England), 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
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- CAZyme3D: A Database of 3D Structures for Carbohydrate-active Enzymes.Journal of molecular biology · 2025Article
- The Early Evolution of Tudor Genes in Holozoa and How Their Distribution Was Influenced by Life History Traits in Metazoa.Genome biology and evolution · 2025Article
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- Architecture, Function, Regulation, and Evolution of α-Glucans Metabolic Enzymes in Prokaryotes.Chemical reviews · 2024Review
- Evolution and phylogenetic distribution of endo-α-mannosidase.Glycobiology · 2023Article
- The origin of the expressed retrotransposed gene ACTBL2 and its influence on human melanoma cells' motility and focal adhesion formation.Scientific reports · 2021Article
- Article
- Deep evolutionary analysis reveals the design principles of fold A glycosyltransferases.eLife · 2020Article
- Whole Genome Enabled Phylogenetic and Secretome Analyses of TwoThe plant pathology journal · 2020Article
- Tracing the origin and evolution of pseudokinases across the tree of life.Science signaling · 2019Article
- Profile Comparer Extended: phylogeny of lytic polysaccharide monooxygenase families using profile hidden Markov model alignments.F1000Research · 2019Article
- A sequence family database built on ECOD structural domains.Bioinformatics (Oxford, England) · 2018Article
- Reconstruction of the sialylation pathway in the ancestor of eukaryotes.Scientific reports · 2018Article
- Tangled history of a multigene family: The evolution of ISOPENTENYLTRANSFERASE genes.PloS one · 2018Article
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Authors and funding
6 authors.
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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. Availability and Implementation: This software is implemented in C/C ++ and is available at http://cys.bios.niu.edu/pHMM-Tree/source/. Contact: zhanghan@nankai.edu.cn or yyin@niu.edu. Supplementary information: Supplementary data are available at Bioinformatics online.
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