2004/05/19 by B. Barbiellini, Alexandra Portnova, Barbiellini, B. +7
Biochemistry, Genetics and Molecular Biology · Physics and Astronomy · #FOS: Biological sciences #FOS: Physical sciences #Genomics (q-bio.GN) #Genomics and Phylogenetic Studies #Machine Learning in Bioinformatics #Populations and Evolution (q-bio.PE) #RNA and protein synthesis mechanisms #Statistical Mechanics (cond-mat.stat-mech) #cond-mat.stat-mech #q-bio.GN #q-bio.PE
paper · pdf · doi:10.48550/arxiv.q-bio/0405016
Paper presented at the Biological Language Conference November 20-21, 2003 University of Pittsburgh
arxiv created 2004/05/19 · openalex publication_date 2004/05/19 · arxiv updated 2009/12/01 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28
Evolutionary models measure the probability of amino acid substitutions occurring over different evolutionary distances. We examine various evolutionary models based on empirically derived amino acid substitution matrices. The models are constructed using the PAM and BLOSUM amino acid substitution matrices. We rescale these matrices by raising them to powers to model substitution patterns that account for different evolutionary distances. We also examine models that account for the dissimilarity of substitution rates along a protein sequence. We compare the models by computing the likelihood of each model across different alignments. We also present a specific example to illustrate the subtle differences in the estimation of evolutionary distance computed using the different models.