UCEasy: A software package for automating and simplifying the analysis of ultraconserved elements (UCEs)

Area of Science:

• Genomics
• Bioinformatics
• Evolutionary Biology

Background:

• Ultraconserved Elements (UCEs) are valuable genetic markers for phylogenomics.
• Current in silico analysis of UCEs involves complex, heterogeneous bioinformatics tools.
• This complexity poses a challenge for researchers lacking specialized bioinformatics training.

Purpose of the Study:

• To develop an accessible software package for the computational analysis of UCEs.
• To improve the reproducibility of phylogenomic studies using UCE data.
• To standardize and simplify the UCE data analysis workflow.

Main Methods:

• UCEasy is presented as an easy-to-install software package with a command-line interface.
• It acts as a wrapper to automate and standardize quality control, assembly, and UCE extraction/alignment.
• The software follows best practices in research software development.

Main Results:

• UCEasy generates a data matrix of UCEs with varying completeness levels.
• The software was successfully used to reproduce published phylogenomic results.
• Demonstrated functionality on genomic datasets from *Turdus* (Aves) and Adephaga (Coleoptera).

Conclusions:

• UCEasy facilitates the computational analysis of UCEs from sequencing samples.
• The tool enhances reproducibility by standardizing and automating complex bioinformatics workflows.
• UCEasy provides a user-friendly solution for extracting UCEs for phylogenetic inference.