Biology – Quantitative Biology – Genomics
Scientific paper
2009-11-15
Biology
Quantitative Biology
Genomics
Scientific paper
We present an Evolutionary Placement Algorithm (EPA) for the rapid assignment of sequence fragments (short reads) to branches of a given phylogenetic tree under the Maximum Likelihood (ML) model. The accuracy of the algorithm is evaluated on several real-world data sets and compared to placement by pair-wise sequence comparison, using edit distances and BLAST. We test two versions of the placement algorithm, one slow and more accurate where branch length optimization is conducted for each short read insertion and a faster version where the branch lengths are approximated at the insertion position. For the slow version, additional heuristic techniques are explored that almost yield the same run time as the fast version, with only a small loss of accuracy. When those additional heuristics are employed the run time of the more accurate algorithm is comparable to that of a simple BLAST search for data sets with a high number of short query sequences. Moreover, the accuracy of the Evolutionary Placement Algorithm is significantly higher, in particular when the taxon sampling of the reference topology is sparse or inadequate. Our algorithm, which has been integrated into RAxML, therefore provides an equally fast but more accurate alternative to BLAST for phylogeny-aware analysis of short-read sequence data.
Berger S. A.
Stamatakis Alexandros
No associations
LandOfFree
Evolutionary Placement of Short Sequence Reads does not yet have a rating. At this time, there are no reviews or comments for this scientific paper.
If you have personal experience with Evolutionary Placement of Short Sequence Reads, we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and Evolutionary Placement of Short Sequence Reads will most certainly appreciate the feedback.
Profile ID: LFWR-SCP-O-323834