Related Experiment Video
Updated: Jul 2, 2026

A Practical Guide to Phylogenetics for Nonexperts
Published on: February 5, 2014
Phylogenetic profiles reveal evolutionary relationships within the "twilight zone" of sequence similarity
Gue Su Chang1, Yoojin Hong, Kyung Dae Ko
1Department of Biology, Pennsylvania State University, State College, PA 16802, USA.
Abstract:
Inferring evolutionary relationships among highly divergent protein sequences is a daunting task. In particular, when pairwise sequence alignments between protein sequences fall <25% identity, the phylogenetic relationships among sequences cannot be estimated with statistical certainty. Here, we show that phylogenetic profiles generated with the Gestalt Domain Detection Algorithm-Basic Local Alignment Tool (GDDA-BLAST) are capable of deriving, ab initio, phylogenetic relationships for highly divergent proteins in a quantifiable and robust manner. Notably, the results from our computational case study of the highly divergent family of retroelements accord with previous estimates of their evolutionary relationships. Taken together, these data demonstrate that GDDA-BLAST provides an independent and powerful measure of evolutionary relationships that does not rely on potentially subjective sequence alignment. We demonstrate that evolutionary relationships can be measured with phylogenetic profiles, and therefore propose that these measurements can provide key insights into relationships among distantly related and/or rapidly evolving proteins.
Related Concept Videos
Evolutionary Relationships through Genome Comparisons
Microbial Phylogeny
Gene Evolution - Fast or Slow?
In contrast, regions which code...
Gene Evolution - Fast or Slow?
In contrast, regions which code...
Phylogenetic Trees
Phylogenetic Trees

