Rute da Fonseca
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When dealing with non-model organisms it is not always easy to choose the best approach given a specific biological question, a limited budget, and challenging sample material. Furthermore, although recent advances in technology offer unprecedented opportunities for research in non-model organisms, they also demand unprecedented awareness from the researcher regarding the assumptions and limitations of each method.
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In this review published in Marine Genomics we present an overview of the current sequencing technologies and the methods used in typical high-throughput data analyses pipelines.
One of my main contributions to the bird phylogenomic effort was a tool to find problematic regions in the multiple sequence alignments, which was afterwards improved by Lisandra Zepeda and resulted in this companion paper.