UCEasy

UCEasy automates analysis of ultraconserved elements (UCEs) to extract, assemble, align, and generate UCE data matrices for phylogenomic inference.

Key Features:

• Automation: Automates stages of UCE data processing including quality control, assembly, extraction, and alignment.
• Standardization and Quality Control: Standardizes quality control of raw sequencing reads, assembly workflows, and UCE extraction and alignment to ensure consistent results.
• Data Matrix Generation: Generates data matrices reflecting varying levels of completeness for downstream phylogenetic analyses.
• Reproducibility and Best Practices: Adheres to best practices to enhance reproducibility of computational experiments.

Scientific Applications:

• Phylogenomic inference: Enables inference of evolutionary relationships using UCE-derived data matrices.
• Reproduction of published studies: Has been used to reproduce published phylogenomic results, including analyses of the bird genus Turdus (Aves) and Adephaga (Coleoptera).

Methodology:

Performs quality control of raw sequencing reads, assembly processes, extraction and alignment of UCEs, and generation of UCE data matrices.