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Initially the alignment was divided into partitions based on coding position.
The light phenotype is determined by homozygosity of a single recessive amino acid change (G → T transversion) at coding position 869 in the TYRP1 gene [ 11].
The mutation in our patient was at amino coding position 633, which is closest to subject #3 reported by Bainbridge et al. [ 23] (659_660del).
The chimpanzee Ugt1a2 has a complete open reading frame suggesting being a functional gene while the human UGT1A2 has a single-nt deletion at coding position 127 causing a frameshift.
When two individuals are compared, haplotypes are concatenated, so that each coding position in the model contributes four times, once for each pairing of haplotype in one individual to haplotype in the other individual.
In contrast, the human UGT1A5 is a functional gene while the chimpanzee Ugt1a5 appears to be a pseudogene because its sequences have a single-nt deletion at coding position 704.
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Blekhman et al. demonstrated that coding positions within disease associated genes underlying a number of complex human diseases are more rapidly evolving than coding regions of genes not associated with disease [8].
Substitution models for coding positions 1+2 (CP12) and CP3 were unlinked, and substitution models in each coding position were selected by Akaike Information Criterion in jModeltest (23 ).
In group 1, three subgroups with DNPs in coding positions were identified.
We first trained the model using 14 649 protein coding positions for which we generated matching Affymetrix SNP6.0 calls.
Distribution of SNPs with respect to coding positions was calculated using KaKs-calculator v.1.2 (Zhang et al. 2006).
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