BpWrapper: BioPerl-based sequence and tree utilities for rapid prototyping of bioinformatics pipelines

Area of Science:

• Bioinformatics
• Computational Biology
• Genomics

Background:

• Automated bioinformatics workflows benefit from command-line utilities for robustness, maintainability, and reproducibility.
• Existing command-line tools often lack integration with popular open-source biological software toolkits like BioPerl.
• A need exists for accessible command-line interfaces to leverage established biological software libraries.

Purpose of the Study:

• To develop command-line utilities that provide access to BioPerl module functionality.
• To simplify the manipulation of molecular sequences, alignments, phylogenetic trees, and DNA polymorphisms.
• To enable bioinformaticians to rapidly prototype workflows without custom scripting.

Main Methods:

• Development of BpWrapper, a suite of command-line utilities for UNIX-family operating systems.
• Initial release includes bioseq, bioaln, biotree, and biopop for specialized sequence data manipulation.
• Incorporation of over a hundred methods as command-line options, with easy extensibility.

Main Results:

• BpWrapper offers accessible command-line access to BioPerl functionality for novice and experienced users.
• Utilities support manipulation of molecular sequences, alignments, phylogenetic trees, and DNA polymorphisms.
• Performance is comparable to other BioPerl-based utilities and lags behind precompiled tools.

Conclusions:

• BpWrapper enhances existing sequence utilities with Unix design principles: concise UI, extensive options, and standard I/O.
• Provides novel methods for sequence, alignment, and tree manipulation not found in tools like EMBOSS or Newick Utilities.
• BpWrapper is valuable for rapid command-line workflow prototyping in comparative genomics and other bioinformatics applications.