Name

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

Introduction

Here we provide Perl Module Bio::BPWrapper, command-line utilities and Perl Modules which wrap Bio::Perl. See the Qui 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:

bioseq

a wrapper of BioPerl class Bio::Seq with additional methods

bioaln

a wrapper of Bio::SimpleAlign which inherits Bio::Seq and additional methods)

biopop

a wrapper of Bio::PopGen which can be converted from Bio::SimpleAlign and additional methods)

biotree

a wrapper of 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