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 web platform dedicated to integrative species delimitation.
Spart Explorer is structured around a three-step workflow: 1) exploration of species limits, currently through two single-locus species delimitation approaches (ABGD and ASAP); 2) integration and visualization of the resulting species partitions through a dynamic segmented bar chart, and 3) statistical comparisons of alternative species partitions (LIMES), whether inferred on the platform, or downloaded from local files (for example, to compare a new partition with those previously inferred from morphological data, based on geographical distribution or representing the current taxonomic status of the studied organisms).
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.
