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@article{Ratmann:2017:molbev/msx263,
author = {Ratmann, O and Ha, Minh Lam and Boni, MF},
doi = {molbev/msx263},
journal = {Molecular Biology and Evolution},
pages = {247--251},
title = {Improved algorithmic complexity for the 3SEQ recombination detection algorithm},
url = {http://dx.doi.org/10.1093/molbev/msx263},
volume = {35},
year = {2017}
}

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TY  - JOUR
AB  - Identifying recombinant sequences in an era of large genomic databases is challenging as it requires an efficient algorithm to identify candidate recombinants and parents, as well as appropriate statistical methods to correct for the large number of comparisons performed. In 2007, a computation was introduced for an exact nonparametric mosaicism statistic that gave high-precision p-values for putative recombinants. This exact computation meant that multiple-comparisons corrected p-values also had high precision, which is crucial when performing millions or billions of tests in large databases. Here, we introduce an improvement to the algorithmic complexity of this computation from O(mn3) to O(mn2), where m and n are the numbers of recombination-informative sites in the candidate recombinant. This new computation allows for recombination analysis to be performed in alignments with thousands of polymorphic sites. Benchmark runs are presented on viral genome sequence alignments, new features are introduced, and applications outside recombination analysis are discussed.
AU  - Ratmann,O
AU  - Ha,Minh Lam
AU  - Boni,MF
DO  - molbev/msx263
EP  - 251
PY  - 2017///
SN  - 1537-1719
SP  - 247
TI  - Improved algorithmic complexity for the 3SEQ recombination detection algorithm
T2  - Molecular Biology and Evolution
UR  - http://dx.doi.org/10.1093/molbev/msx263
UR  - http://hdl.handle.net/10044/1/52176
VL  - 35
ER  -

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