Accurate reconstruction of insertion-deletion histories by statistical phylogenetics.
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 fi...
| Main Authors: | , , , |
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| Format: | Journal article |
| Language: | English |
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Public Library of Science
2012
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| _version_ | 1797092901102026752 |
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| author | Westesson, O Lunter, G Paten, B Holmes, I |
| author_facet | Westesson, O Lunter, G Paten, B Holmes, I |
| author_sort | Westesson, O |
| collection | OXFORD |
| description | 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 several methods for reconstruction of indel history. The methods tested include a relatively new algorithm for statistical marginalization of MSAs that sums over a stochastically-sampled ensemble of the most probable evolutionary histories. For mammalian evolutionary parameters on several different trees, the single most likely history sampled by our algorithm appears less biased than histories reconstructed by other MSA methods. The algorithm can also be used for alignment-free inference, where the MSA is explicitly summed out of the analysis. As an illustration of our method, we discuss reconstruction of the evolutionary histories of human protein-coding genes. |
| first_indexed | 2024-03-07T03:52:38Z |
| format | Journal article |
| id | oxford-uuid:c1cd3a63-2e20-4321-b779-666a9e71b7e0 |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-03-07T03:52:38Z |
| publishDate | 2012 |
| publisher | Public Library of Science |
| record_format | dspace |
| spelling | oxford-uuid:c1cd3a63-2e20-4321-b779-666a9e71b7e02022-03-27T06:04:13ZAccurate reconstruction of insertion-deletion histories by statistical phylogenetics.Journal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:c1cd3a63-2e20-4321-b779-666a9e71b7e0EnglishSymplectic Elements at OxfordPublic Library of Science2012Westesson, OLunter, GPaten, BHolmes, IThe 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 several methods for reconstruction of indel history. The methods tested include a relatively new algorithm for statistical marginalization of MSAs that sums over a stochastically-sampled ensemble of the most probable evolutionary histories. For mammalian evolutionary parameters on several different trees, the single most likely history sampled by our algorithm appears less biased than histories reconstructed by other MSA methods. The algorithm can also be used for alignment-free inference, where the MSA is explicitly summed out of the analysis. As an illustration of our method, we discuss reconstruction of the evolutionary histories of human protein-coding genes. |
| spellingShingle | Westesson, O Lunter, G Paten, B Holmes, I Accurate reconstruction of insertion-deletion histories by statistical phylogenetics. |
| title | Accurate reconstruction of insertion-deletion histories by statistical phylogenetics. |
| title_full | Accurate reconstruction of insertion-deletion histories by statistical phylogenetics. |
| title_fullStr | Accurate reconstruction of insertion-deletion histories by statistical phylogenetics. |
| title_full_unstemmed | Accurate reconstruction of insertion-deletion histories by statistical phylogenetics. |
| title_short | Accurate reconstruction of insertion-deletion histories by statistical phylogenetics. |
| title_sort | accurate reconstruction of insertion deletion histories by statistical phylogenetics |
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