PhylotaR: An Automated Pipeline for Retrieving Orthologous DNA Sequences from GenBank in R.

ABSTRACT: The exceptional increase in molecular DNA sequence data in open repositories is mirrored by an ever-growing interest among evolutionary biologists to harvest and use those data for phylogenetic inference. Many quality issues, however, are known and the sheer amount and complexity of data available can pose considerable barriers to their usefulness. A key issue in this domain is the high frequency of sequence mislabeling encountered when searching for suitable sequences for phylogenetic analysis. These issues include, among others, the incorrect identification of sequenced species, non-standardized and ambiguous sequence annotation, and the inadvertent addition of paralogous sequences by users. Taken together, these issues likely add considerable noise, error or bias to phylogenetic inferen

SUBMITTER: Bennett DJ 

PROVIDER: S-EPMC6027284 | biostudies-literature | 2018 Jun

REPOSITORIES: biostudies-literature