discromark

discromark identifies and designs nuclear DNA (nDNA) phylogenetic markers from orthologous sequences derived from whole-genome or whole-transcriptome data.

Key Features:

• Automated Workflow: Automates discovery and design of nDNA markers from input orthologous sequences.
• Local alignment and trimming: Performs local alignment and alignment trimming to refine multiple sequence alignments.
• Reference mapping: Maps refined sequences against reference genomes to ensure accuracy in marker identification.
• Primer design from MSAs: Designs primer pairs based on processed multiple sequence alignments to amplify target regions across taxa.
• Versatility across species groups: Effective for closely and distantly related species, identifying 78 markers in Cloeon dipterum s.l. and designing primer pairs for 23 markers across several families within the insect order Ephemeroptera.
• Phylogenetic outputs: Produces exon sequence alignments that can be used to reconstruct well-supported phylogenies and infer structured haplotype networks.

Scientific Applications:

• Phylogenetic inference: Enables reconstruction of phylogenies and haplotype networks using exon alignments derived from nDNA markers.
• Evolutionary biology analyses: Facilitates comparative analyses of nuclear loci across taxa to study evolutionary relationships.
• Biodiversity assessments: Supports marker development for genetic surveys across closely related species complexes and broader taxonomic orders.

Methodology:

Integrates local alignment, alignment trimming, reference-genome mapping, and primer design based on multiple sequence alignments of orthologous sequences from whole-genome or whole-transcriptome data.