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Branch-site models Allow ω vary among branches. Likelihood ratio test (LRT) • LRT based on χ 2 can be powerful 2Δl = 2 (l 1-l 2) χ 2 distribution Alternative model (estimated ω 2>1) Null model (fixed ω 2=1) • Power is affected by (i) sequence divergence, (ii) number of lineages, and (iii) strength of positive selection • The most efficient way to increase power is to add lineages Anisimova, Bielawski, and Yang, 2001, Mol. Bio. Evol. 18:1585-1592.
Requirements for PAML Analysis • A coding DNA sequence alignment in PAML format. • A treefile in newick-like format. • codeml.ctl parameter file. • PAML installed on your machine! Searching DNA sequences Download of coding sequences from different species by querying databases such as: • UniProt (http://www.uniprot.org/) • NCBI Entrez Gene (http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene) • Genome browser Ensembl (http://www.ensembl.org/).
Page 1 and 2: PAML Phylogenetic Analysis by Maxim
Page 3 and 4: Amino Acid Sites Subject to Positiv
Page 5 and 6: Metodi di Maximum Likelihood • In
Page 7 and 8: Site-specific models Allow ω vary
Page 9: H 0: Beta distributed variable sele
Page 13 and 14: Coding DNA sequence alignment in PA
Page 15 and 16: CODEML.ctl parameter file • Zihen
Page 17 and 18: Output Files Several different outp

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