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Treefile • Tree must be trifurcated NOT rooted. • The tree is likely to represent the true relationship among the species • NCBITaxonomy (http://www.ncbi.nlm.nih.gov/guide/taxonomy/ ). • Tree exported in *.phy. • Converted from rooted to unrooted as suggest the author with Retree tools of Phylip. MEGA4 - http://www.megasoftware.net/ Phylip - http://evolution.genetics.washington.edu/phylip.html Abbreviazioni: PCA: Procavia capensis PVA: Pteropus vampyrus MLU: Myotis lucifugus BTA: Bos taurus SSC: Sus scrofa TTR: Tursiops truncatus FCA: Felis catus CFA: Canis familiaris STO: Spermophilus tridecemlineatus RNO: Rattus norvegicus MUS: Mus musculus OPR: Ochotona princeps PAB: Pongo abelii HOM: Homo sapiens GGO: Gorilla gorilla CJA: Callithrix jacchus
CODEML.ctl parameter file • Ziheng Yang: Computational Molecular Evolution • PAML User Guide k → transition/transversion rate ratio π → codon frequency • Yang Z, Nielsen R. Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. Mol Biol Evol 2000; 17: 32-43 • Yang Z. PAML 4: phylogenetic Analysis by Maximum Likelihood. Mol Biol Evol 2007; 24: 1586-1591 • F EQUAL: each codon has the same frequency • F1X 4: codon frequency are expected from the frequencies of four nucleotides. • F3 X 4: codon frequencies are expected from 3 sets of nucleotide frequencies for the three codon positions. • F61: all codon frequnecies as parameters
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 and 10: H 0: Beta distributed variable sele
Page 11 and 12: Requirements for PAML Analysis •
Page 13: Coding DNA sequence alignment in PA
Page 17 and 18: Output Files Several different outp

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