iTaxoTools

iTaxoTools provides computational tools for species delimitation, diagnosis, and data management to support alpha-taxonomic research.

Key Features:

• Species delimitation: Integrates ABGD, ASAP, DELINEATE, GMYC, PTP, tr2 and a simple threshold-clustering delimitation method for delimiting species from genetic data.
• Pairwise distance computation: Computes pairwise DNA distances from molecular sequence data.
• Ultrametric tree construction: Constructs ultrametric time trees using non-parametric rate smoothing.
• Diagnostic nucleotide identification: Identifies species-diagnostic nucleotide positions.
• Morphometric analyses: Performs standard morphometric analyses for phenotypic data.
• Sequence and data format conversion: Converts among molecular sequence formats, geographical coordinate formats, and measurement units.
• File and table operations: Merges, splits, and prunes sequence files and tables.
• Statistical tests: Provides simple statistical tests for data analysis.
• Implementation: Implemented in Python and distributed as open-source code.

Scientific Applications:

• Species delimitation and diagnosis: Supports delimiting and diagnosing species using genetic and morphometric evidence.
• Taxonomic hypothesis generation: Produces species hypotheses for taxonomic descriptions and revisions.
• Preparation of phylogenetic and temporal analyses: Generates pairwise distances and ultrametric trees for downstream phylogenetic and time-tree analyses.
• Diagnostic character detection: Supplies nucleotide positions and morphometric differences for formal species diagnoses.
• Biodiversity and conservation research: Contributes data products and species hypotheses useful for biodiversity inventories and conservation planning.

Methodology:

Implements ABGD, ASAP, DELINEATE, GMYC, PTP, tr2 and a threshold-clustering delimitation; computes pairwise DNA distances; constructs ultrametric trees via non-parametric rate smoothing; identifies diagnostic nucleotide positions; performs morphometric analyses; converts sequence formats, coordinates and units; merges, splits and prunes sequence files and tables; and provides simple statistical tests, implemented in Python and released as open-source code.