Measuring Phylogenetic Information of Incomplete Sequence Data.

ABSTRACT: Widely used approaches for extracting phylogenetic information from aligned sets of molecular sequences rely upon probabilistic models of nucleotide substitution or amino-acid replacement. The phylogenetic information that can be extracted depends on the number of columns in the sequence alignment and will be decreased when the alignment contains gaps due to insertion or deletion events. Motivated by the measurement of information loss, we suggest assessment of the effective sequence length (ESL) of an aligned data set. The ESL can differ from the actual number of columns in a sequence alignment because of the presence of alignment gaps. Furthermore, the estimation of phylogenetic information is affected by model misspecification. Inevitably, the actual process of molecular evolution diffe

SUBMITTER: Seo TK 

PROVIDER: S-EPMC9226685 | biostudies-literature | 2022 Apr

REPOSITORIES: biostudies-literature