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1 non-PAUSE user
Author image Rocky Bernstein
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This file located in the distribution. But it is also found in a github project wiki: https://github.com/bioperl/p5-bwrapper/wiki/BPWrapper where we can immediately see the results and others can contribute.


Bio::BPWrapper -- command-line utilities for Bio::Perl


Here we provide Perl Module Bio::BPWrapper, command-line utilities and Perl Modules which wrap Bio::Perl. See the Qiu Lab Bioutils wiki for more detailed information.

What is this?

The main suite of is a series of command-line scripts written in Perl that provide convenient command-line access to popular Bio::Perl methods.

Designed as UNIX utilities, these tools aim to circumvent a constant need (and urge) to write one-off Bio::Perl scripts for routine manipulations of sequences, alignments and trees. And, of course, command-line tools are super-fast ways for data manipulation and exploration For the virtues of command-line tools see the O'Reilly Book: Data Science at Command Line by Jeroen Janssens.

There are a few interconnected command-line scripts:


command-line access to BioPerl class Bio::Seq with additional methods


command-line access to Bio::SimpleAlign which inherits Bio::Seq and additional methods)


command-line access to Bio::PopGen which can be converted from Bio::SimpleAlign and additional methods)


command-line access to Bio::TreeIO, Bio::Tree::Tree, and Bio::Tree::Node with additional methods

These utilities have been in development since Fall 2002 in Dr. Weigang Qiu's lab at Hunter College of the City University of New York.

We welcome and encourage all developers to contribute any BioPerl-based utilities to this repository.

See also

Bio::BPWrapper::AlnManipulations, Bio::BPWrapper::PopManipulations, Bio::BPWrapper::SeqManipulations