2011/02/09 by David Koslicki, Koslicki, David
Biochemistry, Genetics and Molecular Biology · Computer Science · #Algorithms and Data Compression #FOS: Biological sciences #Genomics and Phylogenetic Studies #Populations and Evolution (q-bio.PE) #Quantitative Methods (q-bio.QM) #RNA and protein synthesis mechanisms #q-bio.PE #q-bio.QM
paper · pdf · doi:10.48550/arxiv.1102.1897
14 pages
arxiv created 2011/02/09 · openalex publication_date 2011/02/09 · arxiv updated 2011/02/10 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28
We present a comprehensive new framework for handling biologically accurate models of molecular evolution. This model provides a systematic framework for studying models of molecular evolution that implement heterogeneous rates, conservation of reading frame, differing rates of insertion and deletion, customizable parametrization of the probabilities and types of substitutions, insertions, and deletions, as well as neighboring dependencies. We have stated the model in terms of an infinite state Markov chain in order to maximize the number of applicable theorems useful in the analysis of the model. We use such theorems to develop an alignment-free parameter estimation technique. This alignment-free technique circumvents many of the nuanced issues related to alignment-dependent estimation. We then apply an implementation of our model to reproduce (in a completely alignment-free fashion) some observed results of Zhang and Gerstein (2003) regarding indel length distribution in human ribosomal protein pseudogenes.