Delimitation
Cluster DNA sequences into species hypotheses
Spart explorer
A taxonomic web platform to
infer, compare and visualize species partitions
Spart Explorer is a user-friendly tool which infers species hypotheses based on DNA sequences, using two popular species delimitation tools, ABGD and ASAP. The platform also implements LIMES, which can compare different partitions. Species partitions obtained on the platform or uploaded from local files can then be compared in a dynamic and intuitive graphic representation, associated to a phylogenetic tree, to facilitate result interpretation and comparison in an integrative taxonomy framework.
Visualisation and comparison
Visualize, merge and compare various species partition file
Tools used in Spart Explorer
ABGD
ABGD (Automatic Barcode Gap Discovery) is a fast, simple method to split a sequence alignment data set into species hypotheses. The method uses a distance threshold estimated from the distribution of genetic distances between specimens from the same species (intraspecific diversity) and from different species (interspecific diversity).
ASAP
ASAP (Assemble Species by Automatic Partitioning) implements of a hierarchical clustering algorithm that only uses pairwise genetic distances, thus avoiding the computational burden of phylogenetic reconstruction, to propose species hypotheses. ASAP proposes species partitions ranked by a scoring system that uses no biological prior insight of intraspecific diversity.
LIMES
LIMES is an automatic calculation tool which qualitatively compares species partitions obtained by distinct SD approaches, regardless of their respective theoretical backgrounds, and even in absence of reference topology. LIMES can also merge, extract and export SPART files.
