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CZ5226: Advanced Bioinformatics Lecture 6: HHM Method for generating motifs Prof.

A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. This program also calculates the relative importance and model-averaged estimates of substitution parameters, including a model-averaged estimate of the phylogeny.The Birnaviridae genome encodes several proteins: Birnaviridae RNA-directed RNA polymerase (VP1), which lacks the highly conserved Gly-Asp-Asp (GDD) sequence, a component of the proposed catalytic site of this enzyme family that exists in the conserved motif VI of the palm domain of other RNA-directed RNA polymerases.Infectious pancreatic necrosis virus (IPNV), a birnavirus, is an important pathogen in fish farms.In-depth reviews about model selection in phylogenetics are available elsewhere (Johnson and Omland 2003; Posada and Buckley 2004; Sullivan and Joyce 2005).Indeed, the performance of different model selection strategies has been the subject of active research (Posada 2001; Posada and Crandall 2001; Pol 2004; Abdo et al. Several programs already exist for the statistical selection of models of nucleotide substitution (e.g., Nylander 2004; Keane et al. Among these, Modeltest (Posada and Crandall 1998) has been one of the most popular.

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