Indel information eliminates trivial sequence alignment in maximum likelihood phylogenetic analysis.
| Autor: | Denton JSS; Division of Vertebrate Zoology, American Museum of Natural History, New York, NY 10024, USA.; Richard Gilder Graduate School, American Museum of Natural History, New York, NY 10024, USA., Wheeler WC; Richard Gilder Graduate School, American Museum of Natural History, New York, NY 10024, USA.; Division of Invertebrate Zoology, American Museum of Natural History, New York, NY 10024, USA. |
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| Jazyk: | angličtina |
| Zdroj: | Cladistics : the international journal of the Willi Hennig Society [Cladistics] 2012 Oct; Vol. 28 (5), pp. 514-528. Date of Electronic Publication: 2012 May 04. |
| DOI: | 10.1111/j.1096-0031.2012.00402.x |
| Abstrakt: | Although there has been a recent proliferation in maximum-likelihood (ML)-based tree estimation methods based on a fixed sequence alignment (MSA), little research has been done on incorporating indel information in this traditional framework. We show, using a simple model on a single character example, that a trivial alignment of a different form than that previously identified for parsimony is optimal in ML under standard assumptions treating indels as "missing" data, but that it is not optimal when indels are incorporated into the character alphabet. We show that the optimality of the trivial alignment is not an artefact of simplified theory assumptions by demonstrating that trivial alignment likelihoods of five different multiple sequence alignment datasets exhibit this phenomenon. These results demonstrate the need for use of indel information in likelihood analysis on fixed MSAs, and suggest that caution must be exercised when drawing conclusions from software implementations claiming improvements in likelihood scores under an indels-as-missing assumption. © The Willi Hennig Society 2012. (© The Willi Hennig Society 2012.) |
| Databáze: | MEDLINE |
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