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• W615931334 abstract "Simulation remains a very important approach to testing the robustness and accuracy of phylogeneticinference methods. However, current simulation programs are limited, especially concerning realisticmodels for simulating insertions and deletions (indels). In this thesis I implement a new, portable andflexible application, named INDELible, which can be used to generate nucleotide, amino acid andcodon sequence data by simulating indels (under several models of indel length distribution) as wellas substitutions (under a rich repertoire of substitution models).In particular, I introduce a simulation study that makes use of one of INDELible’s many uniquefeatures to simulate data with indels under codon models that allow the nonsynonymous/synonymoussubstitution rate ratio to vary among sites and branches. This data is used to quantify, for the firsttime, the precise effects of indels and alignment errors on the false-positive rate and power of thewidely used branch-site test of positive selection. Several alignment programs are used and assessedin this context. Through the simulation experiment, I show that insertions and deletions do not causethe test to generate excessive false positives if the alignment is correct, but alignment errors can leadto unacceptably high false positives. Previous selection studies that use inferior alignment programsare revisited to demonstrate the applicability of my results in real world situations.Further work uses simulated data from INDELible to examine the effects of tree-shape and branchlength on the alignment accuracy of several alignment programs, and the impact of alignment errorson different methods of phylogeny reconstruction. In particular, analysis is performed to explorewhich programs avoid generating the kind of alignment errors that are most detrimental to the processof phylogeny reconstruction." @default.
• W615931334 created "2016-06-24" @default.
• W615931334 creator A5063943904 @default.
• W615931334 date "2011-03-28" @default.
• W615931334 modified "2023-09-26" @default.
• W615931334 title "Computational statistics in molecular phylogenetics" @default.
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