Easy353

Easy353 recovers the Angiosperms353 gene set (AGS), a set of 353 universal low-copy nuclear genes selected from over 600 angiosperm species, from high-throughput sequencing data for phylogenetic and population genetics analyses.

Key Features:

• Target set: Targets the Angiosperms353 gene set (353 universal low-copy nuclear genes) selected from over 600 angiosperm species.
• Assembly strategy: Uses a reference-guided assembly approach to recover target genes from sequencing reads.
• Input data types: Processes diverse high-throughput sequencing data, including genome skimming, RNA-seq, and target enrichment datasets.
• Validation: Evaluated with both simulated and empirical data to assess performance.
• Assembly accuracy: Demonstrates low rates of assembly errors based on evaluation datasets.

Scientific Applications:

• Phylogenetics: Recovers nuclear loci for reconstructing phylogenetic relationships across angiosperms.
• Population genetics: Recovers low-copy nuclear genes useful for population-genetic analyses at multiple taxonomic scales.

Methodology:

Reference-guided assembly of high-throughput sequencing data (genome skimming, RNA-seq, target enrichment) with evaluation using simulated and empirical datasets to quantify assembly error rates.