Bioutils

BioPerl-based Sequence Utilities

Figure 1. Design and Methods of bioutils

What is bioutils?

bioutils are a suite of Perl wrappers that provide convenient command-line accesses to popular BioPerl methods. Designed as UNIX-like utilities, these tools aim to circumvent the need for composing one-off BioPerl scripts for routine manipulations of sequences, alignments and trees.

The initial release of bioutils consists of four utilities (Fig 1):

1. bioseq: a wrapper providing one-letter switches to Bio::Seq methods
2. bioaln: a wrapper providing one-letter switches to Bio::SimpleAlign mehtods
3. biopop: a wrapper providing one-letter switches to Bio::PopGen methods
4. biotree: a wrapper providing one-letter switches to Bio::tree methods

These utilities have been developed since 2002 in the lab of Dr Weigang Qiu at Hunter College of the City University of New York. They are the main code base of the Qiu Lab, which specializes in microbial evolutionary genomics. They proved to be useful, highly efficient, and popular among students and researchers. By releasing bioutils as an Open Source tool, we hope to (1) share our experience and (2) invite other developers to join the effort of making BioPerl more accessible.