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tree-hmm specifications

Information


Unique identifier OMICS_07728
Name tree-hmm
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Requirements
Python, Scipy, Matplotlib, PySAM, Cython
Maintained Yes

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Documentation


Maintainer


  • person_outline Xiaohui Xie <>

Publication for tree-hmm

tree-hmm in publications

 (3)
PMCID: 3676395
PMID: 23762278
DOI: 10.1371/journal.pone.0065012

[…] by some program and thus are known only with some level of reliability; it is common for bioinformatics field. the main idea is formulation of the problem as a hidden markov model on a tree (tree hmm, thmm), where the basic continuous-time markov model is expanded with the introduction of emission probabilities of observed data (e.g. prediction scores) for each underlying discrete state. […]

PMCID: 3117352
PMID: 21685080
DOI: 10.1093/bioinformatics/btr241

[…] sequence reconstruction approach (, ) to infer, for each multiple alignment block, the ancestral sequence at each of the 43 internal nodes of the vertebrate phylogenetic tree. the program uses a tree-hmm approach to infer insertions and deletions over the branches of the tree, and then infers substitutions using a context-dependent substitution model. ) and ) have previously shown, using […]

PMCID: 1087829
PMID: 15780137
DOI: 10.1186/1471-2105-6-63

[…] area of research exists in that direction [,,]. a more direct attack to the problem of introducing phylogeny into existing probabilistic models originated with the concept of tree hmms [,]. the tree hmm method models the evolution of the parsing of different sequences through an hmm. this approach is more related with the evolution of transition probabilities, and i will discuss it later […]


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tree-hmm institution(s)
Institute for Genomics and Bioinformatics, University of California, Irvine, CA, USA

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