ASAP: assemble species by automatic partitioning

ASAP: assemble species by automatic partitioning

2021 | Nicolas Puillandre, Sophie Brouillet, Guillaume Achaz
ASAP is a new method for species delimitation using single-locus sequence alignments. It efficiently partitions data sets with up to 10,000 sequences in minutes, using pairwise genetic distances without phylogenetic reconstruction. ASAP ranks species partitions using a novel scoring system, avoiding biological prior knowledge. It is a standalone program with a web interface or downloadable version. Tested on 10 COI barcode data sets and via Monte Carlo simulations, ASAP performs well compared to ABGD, PTP, and GMYC. It is fast, user-friendly, and provides ranked partitions. ASAP is suitable for large single-locus data sets where no species hypothesis is available. It is recommended as a first step in integrative taxonomy, complemented by other methods for robust species delimitation. ASAP's performance is evaluated using real and simulated data, showing its effectiveness in various scenarios. It is particularly effective under radiation models but less so under Yule models. ASAP avoids phylogenetic reconstruction, making it suitable for DNA barcoding projects. It is recommended for use in conjunction with other methods to improve species delimitation accuracy.ASAP is a new method for species delimitation using single-locus sequence alignments. It efficiently partitions data sets with up to 10,000 sequences in minutes, using pairwise genetic distances without phylogenetic reconstruction. ASAP ranks species partitions using a novel scoring system, avoiding biological prior knowledge. It is a standalone program with a web interface or downloadable version. Tested on 10 COI barcode data sets and via Monte Carlo simulations, ASAP performs well compared to ABGD, PTP, and GMYC. It is fast, user-friendly, and provides ranked partitions. ASAP is suitable for large single-locus data sets where no species hypothesis is available. It is recommended as a first step in integrative taxonomy, complemented by other methods for robust species delimitation. ASAP's performance is evaluated using real and simulated data, showing its effectiveness in various scenarios. It is particularly effective under radiation models but less so under Yule models. ASAP avoids phylogenetic reconstruction, making it suitable for DNA barcoding projects. It is recommended for use in conjunction with other methods to improve species delimitation accuracy.
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