Simulating DNA Coding Sequence Evolution with EvolveAGene 3

摘要: Phylogenetic reconstruction based upon multiple alignments of molecular sequences is important to most branches modern biology and central evolution. Understanding the historical relationships among macromolecules depends computer programs that implement a variety analytical methods. Because it impossible know those with certainty, assessment accuracy methods them requires use realistically simulate evolution DNA sequences. EvolveAGene 3 realistic coding sequence simulation program separates mutation from selection allows user set conditions, including variable regions intensity within variation in over branches. Variation includes base substitutions, insertions, deletions. To best my knowledge, only available simulates intact Output true tree resulting corresponding protein A log file reports frequencies each kind substitution, ratio transition transversion indel substitution mutations, numbers silent amino acid replacement mutations. The realism data sets has been assessed by comparing d N /d S ratio, mutations simulated parameters real “gold standard” BaliBase collection structural alignments. Results show produced are very similar sets, therefore can be used evaluate