POTION: an end-to-end pipeline for positive Darwinian selection detection in genome-scale data through phylogenetic comparison of protein-coding genes.
2015
HONGO, J. A. | CASTRO, G. M. de | CINTRA, L. C. | ZERLOTINI, A. | LOBO, F. P. | JORGE A. HONGO | GIOVANNI M. DE CASTRO | LEANDRO CARRIJO CINTRA, CNPTIA | ADHEMAR ZERLOTINI NETO, CNPTIA | FRANCISCO PEREIRA LOBO, CNPTIA.
Abstract: Background: Detection of genes evolving under positive Darwinian evolution in genome-scale data is nowadays a prevailing strategy in comparative genomics studies to identify genes potentially involved in adaptation processes. Despite the large number of studies aiming to detect and contextualize such gene sets, there is virtually no software available to perform this task in a general, automatic, large-scale and reliable manner. This certainly occurs due to the computational challenges involved in this task, such as the appropriate modeling of data under analysis, the computation time to perform several of the required steps when dealing with genome-scale data and the highly error-prone nature of the sequence and alignment data structures needed for genome-wide positive selection detection.
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