Bioutils
BioPerl-based Sequence Utilities
What is bioutils?
bioutils are a suite of Perl wrappers providing convenient command-line accesses to popular BioPerl classes such as Bio::Seq, Bio::SimpleAlign, and Bio::Tree. Designed as UNIX-like command-line utilities, these tools circumvent the need for composing BioPerl scripts for routine, trivial tasks (e.g., translation, reverse-complement, remove gaps, selecting and deleting sequences).
The initial release of bioutils consists of four utilities (Fig 1):
- bioseq: a wrapper providing one-letter switches to Bio::Seq methods
- bioaln: a wrapper providing one-letter switches to Bio::SimpleAlign mehtods
- biopop: a wrapper providing one-letter switches to Bio::PopGen methods
- 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 and popular among students and researchers. With the release of 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 classes more accessible.