iTaxoTools: ASAP Video Tutorial

Here, we present a video tutorial for the iTaxoTools version of ASAP (Assemble Species by Automatic Partitioning), a method designed for constructing species partitions from single locus sequence alignments.

"ASAP is efficient enough to split data sets as large as 104 sequences into putative species in several minutes. Although grounded in evolutionary theory, ASAP is the implementation of a hierarchical clustering algorithm that only uses pairwise genetic distances, avoiding the computational burden of phylogenetic reconstruction. Importantly, ASAP proposes species partitions ranked by a new scoring system that uses no biological prior insight of intraspecific diversity. ASAP is a stand-alone program that can be used either through a graphical web-interface or that can be downloaded and compiled for local usage. We have assessed its power along with three other programs (ABGD, PTP, and GMYC) on 10 real COI barcode data sets representing various degrees of challenge (from small and easy cases to large and complicated data sets). We also used Monte-Carlo simulations of a multispecies coalescent framework to assess the strengths and weaknesses of ASAP and the other programs. Through these analyses, we demonstrate that ASAP has the potential to become a major tool for taxonomists as it proposes rapidly in a full graphical exploratory interface relevant species hypothesis as a first step of the integrative taxonomy process."

▬ Links & Ressources ▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬
► Download iTaxoTools
https://itaxotools.org/download.html

▬ References ▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬
► ASAP
Puillandre, N., Brouillet, S., & Achaz, G. (2021). ASAP: assemble species by automatic partitioning. Molecular Ecology Resources, 21(2), 609-620. https://doi.org/10.1111/1755-0998.13281
► SPART format
Miralles, A., Ducasse, J., Brouillet, S., Flouri, T., Fujisawa, T., Kapli, P., Knowles, L.L., Kumari, S., Stamatakis, A., Sukumaran, J., Lutteropp, S., Vences, M. & Puillandre, N. (2021). SPART, a versatile and standardized data exchange format for species partition information. Molecular Ecology Resources, 22: 430–438. https://doi.org/10.1111/1755-0998.13470
► iTaxoTools
Vences, M., Miralles, A., Brouillet, S., Ducasse, J., Fedosov, A., Kharchev, V., Kostadinov, I., Kumari, S., Patmanidis, S., Scherz, M.D., Puillandre, N. & Renner, S.S. (2021). iTaxoTools 0.1: Kickstarting a specimen-based software toolkit for taxonomists. Megataxa 6: 77–92. https://doi.org/10.1101/2021.03.26.43...

▬ Voiceover ▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬
► text-to-speech AI tool offered by https://elevenlabs.io

▬ Music ▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬
► Music track: Storm by Aylex
► Source: https://freetouse.com/music

▬ Websites ▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬
► TAXON-OMICS - "New approaches to discovering and naming biodiversity"
https://www.taxon-omics.com/
► iTaxoTools: https://itaxotools.org/

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