Bioutils: Difference between revisions
imported>Weigang (Created page with "<span style="color: Seagreen;font-weight:bold;font-size:large;">BioPerl-based Sequence Utilities<span> ==What is ''bioutils''?== ''bioutils'' are a suite of Perl wrappers prov...") |
imported>Weigang |
||
| Line 1: | Line 1: | ||
<span style="color: Seagreen;font-weight:bold;font-size:large;">BioPerl-based Sequence Utilities<span> | <span style="color: Seagreen;font-weight:bold;font-size:large;">BioPerl-based Sequence Utilities<span> | ||
==What is ''bioutils''?== | ==What is ''bioutils''?== | ||
''bioutils'' are a suite of Perl wrappers | ''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'''): | The initial release of ''bioutils'' consists of four utilities ('''Fig 1'''): | ||
| Line 9: | Line 9: | ||
# '''biotree''': a wrapper providing one-letter switches to Bio::tree 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. | 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. | ||
==Demo 1: Basic usage== | ==Demo 1: Basic usage== | ||
Revision as of 03:28, 29 September 2014
BioPerl-based Sequence Utilities
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):
- 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, 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.