Sentence examples for use of phylogenetic methods from inspiring English sources

We discuss the relevance of our findings as it relates to the use of phylogenetic methods in comparative genomics.

The two main approaches depend on the analysis of sequence composition and the use of phylogenetic methods.

We cannot guarantee that other sites in alignments have a homoplasy level low enough for efficient use of phylogenetic methods for long evolutionary distances.

The use of phylogenetic methods that have been developed to take into account nonstationarity in base frequencies using either distance [ 67, 104] or likelihood approaches [ 105] can at least somewhat ameliorate these effects, though not for codon bias issues [ 66, 103].

Most of the discussion centered on the difficulties in use of phylogenetic methods for the analysis of ncRNAs: phylogenetic models used for protein coding genes usually assume that sites evolve independently, but ncRNAs often violate this assumption, owing to the importance of secondary structure conservation.

Subterranean rodent genome and transcriptome data produced by next-generation sequencing facilitate the use of phylogenetic methods to infer non-synonymous and synonymous substitution rates within coding regions, which can reveal changes at the molecular level that are correlated with the dramatic shift from a terrestrial to subterranean habitat.

Sixty-two vertebrate SWS1 opsin nucleotide coding sequences were obtained from GenBank, aligned using ClustalX [ 21], and analyzed using a variety of phylogenetic methods including maximum parsimony [ 22, 23], maximum likelihood [ 24, 25], and Bayesian methods [ 26].

Importantly, the orthology of AMF meiosis-specific was confirmed using a variety of phylogenetic methods and gene homologs from many other organisms.

Using an array of phylogenetic methods, statistical tests, and character sorting analyses, we show that the polyphyly of netrin and sFRP is well supported and cannot be explained by classical phylogenetic reconstruction artifacts.

Several criteria can be used to evaluate the reliability of phylogenetic methods for inferring topologies.

A number of phylogenetic methods may be used to identify homologs and provide further evidence for their relationships.