Detecting phylogenetic relations out from sparse context trees

The goal of this paper is to study the similarity between sequences using a distance between the \emph{context} trees associated to the sequences. These trees are defined in the framework of \emph{Sparse Probabilistic Suffix Trees} (SPST), and can be estimated using the SPST algorithm. We implement...

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Bibliographic Details
Published in:arXiv.org 2008-04
Main Authors: Leonardi, Florencia, Matioli, Sergio R, Armelin, Hugo A, Galves, Antonio
Format: Article
Language:English
Subjects:
Algorithms
Phylogenetics
Proteins
Suffix trees
Transition probabilities
Vertebrates
Online Access:Get full text
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Summary:The goal of this paper is to study the similarity between sequences using a distance between the \emph{context} trees associated to the sequences. These trees are defined in the framework of \emph{Sparse Probabilistic Suffix Trees} (SPST), and can be estimated using the SPST algorithm. We implement the Phyl-SPST package to compute the distance between the sparse context trees estimated with the SPST algorithm. The distance takes into account the structure of the trees, and indirectly the transition probabilities. We apply this approach to reconstruct a phylogenetic tree of protein sequences in the globin family of vertebrates. We compare this tree with the one obtained using the well-known PAM distance.
ISSN:2331-8422