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Accurate reconstruction of insertion-deletion histories by statistical phylogenetics.

Abstract:

The Multiple Sequence Alignment (MSA) is a computational abstraction that represents a partial summary either of indel history, or of structural similarity. Taking the former view (indel history), it is possible to use formal automata theory to generalize the phylogenetic likelihood framework for finite substitution models (Dayhoff's probability matrices and Felsenstein's pruning algorithm) to arbitrary-length sequences. In this paper, we report results of a simulation-based benchmark of seve...

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Publication status:
Published
Peer review status:
Peer reviewed

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Publisher copy:
10.1371/journal.pone.0034572

Authors


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Institution:
University of Oxford
Division:
MSD
Department:
NDM
Sub department:
Human Genetics Wt Centre
Role:
Author
National Human Genome Research Institute More from this funder
National Institutes of Health More from this funder
Publisher:
Public Library of Science Publisher's website
Journal:
PloS one Journal website
Volume:
7
Issue:
4
Article number:
e34572
Publication date:
2012-01-01
DOI:
EISSN:
1932-6203
ISSN:
1932-6203
Source identifiers:
325248
Language:
English
Keywords:
UUID:
uuid:c1cd3a63-2e20-4321-b779-666a9e71b7e0
Local pid:
pubs:325248
Deposit date:
2012-12-19

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