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Files included in the folder:
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mtCDNApri.nuc: codon sequences from 7 apes (small data set in Yang et al. 1998)
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mtCDNApri.trees: tree file for the data
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OmegaAA.dat: file specifying different types of amino acid substitutions
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codeml.ctl: control file
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Also the following two files are incldued (large data set in Yang et al. 1998)
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This directory contains example files for estimating
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nonsynonymous/synonymous substitution rate ratios for different types
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of amino acid changes. The data were used in Yang et al. (1998), so
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you can use the data to duplicate results in that paper.
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(1) Table 5 and the section titled "Different types of amino acid
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substitutions". This model assumes different dn/ds (w) ratios for
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different types of amino acid substitutions. You specify how many
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amino acid substitution types you would like to have and which amino
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acid pairs (changes) should be in each type. The data should be codon
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sequences (seqtype = 1), and the model is specified by aaDist = 7
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(AAClasses). The details of amino acid substitution types are
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specified in a file called OmegaAA.dat. See that file for details.
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The model can be used to fit different rates for "radical" and
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"conserved" amino acid substitutions.
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Yang et al. (1998) implemented the model for codon sequences only
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(seqtype = 1). In theory the model should be applicable to amino acid
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sequences as well (seqtype = 2), with one fewer parameter required.
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However, such models (for amino acid sequences) are either not tested
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properly or never made to work. If you need to apply such models to
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amino acid sequences, you can let me know and I'll try to savalge the model.
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(2) Table 4. Mechanistic models of codon substitution. You should have
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seqtype = 1, model = 0, NSsites = 0. Then the models are specified
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using aaDist as follows. You need to copy files with names like
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g1974c.dat, g1974p.dat, g1974v.dat, g1974a.dat, grantham.dat, or
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miyata.dat into the current folder to run those models.
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aaDist = 1 * geometric relationship using Grantham
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aaDist = 2 * geometric relationship using Miyata & Yasunaga
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aaDist = 3 * geometric relationship using c (composition)
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aaDist = 4 * geometric relationship using p (polarity)
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aaDist = 5 * geometric relationship using v (volume)
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aaDist = 6 * geometric relationship using a (aromaticity)
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aaDist = -1 * linear relationship using Grantham
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aaDist = -2 * linear relationship using Miyata & Yasunaga
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aaDist = -3 * linear relationship using c (composition)
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aaDist = -4 * linear relationship using p (polarity)
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aaDist = -5 * linear relationship using v (volume)
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aaDist = -6 * linear relationship using a (aromaticity)
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(3) Table 3. Mechanistic models of amino acid substitution. As above
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for table 4, but you should have seqtype = 2, model = 6 (FromCodon),
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NSsites = 0. Note that with amino acid sequences only, we cannot
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estimate synonymous rate, and the models have one fewer parameter than
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when codon sequences are used.
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The models were implemented several years ago and not carefully
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maintained since then. So let me know you notice anything strange.
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You should always run the example data set to duplicate the results in
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Yang, Z., R. Nielsen, and M. Hasegawa, 1998. Models of amino acid
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substitution and applications to mitochondrial protein
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evolution. Mol. Biol. Evol. 15: 1600-1611.
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examples/mtCDNA/README.txt
