DOMINO

DOMINO facilitates discovery and genotyping of informative molecular markers from next-generation sequencing (NGS) data and pre-computed sequence alignments for phylogenetic and genome-wide population genetics studies of non-model organisms.

Key Features:

• Input Data Types: Uses next-generation sequencing (NGS) data and pre-computed sequence alignments as inputs.
• Versatile pipeline: Integrates popular NGS tools with novel utilities to enable discovery and selection of personalized molecular markers across taxonomic resolutions.
• Genomic partitioning strategies: Employs genomic partitioning to discover and genotype large numbers of markers simultaneously.
• Taxonomic resolution: Selects markers that are informative at multiple levels of taxonomic resolution.
• Downstream assay templates: Produces marker sequences applicable as templates for PCR amplification across broader taxonomic scope and for bait design in target DNA enrichment.
• Performance evaluation: Evaluated using computer simulations and empirical datasets.

Scientific Applications:

• Phylogenetics: Supports marker discovery and genotyping for phylogenetic studies of non-model organisms.
• Genome-wide population genetics: Enables large-scale marker discovery and genotyping for population genomic analyses.
• Marker development in non-model organisms: Facilitates development of molecular markers when reference resources are limited.
• Assay and enrichment design: Provides marker sequences usable for PCR assay design and bait design for target DNA enrichment.

Methodology:

Integrates NGS tools and novel utilities, accepts NGS data and pre-computed alignments, applies genomic partitioning strategies for marker discovery and genotyping, and evaluates performance via computer simulations and empirical datasets.