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XS-based BioPerl extensions to C libraries (defunct)
C Perl C++

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o Version

 This is Bioperl-ext version 1.3 from CVS HEAD

o Summary

This is the directory for the Bioperl C compiled Extensions.

These currently include:

   Bio::Ext::Align (Ewan Birney <>
                    and Yee Man Chan <>)
   Bio::SeqIO::staden::read (Aaron Mackey <>)

o Installing

 Depending on your choise of extensions, you might need
 Inline::MakeMaker and Inline::C to create the makefile. Use for
 example the cpan program to install Inline::MakeMaker and answer yes
 when prompted to install Inline::C.
 To install all of the extension packages, you can use the top-level
 Makefile.PL (present in the same directory you're reading this README
 from) (Make sure you read the various notes below about each package
 before doing this!):
   perl Makefile.PL
   make test
   make install (may need root permissions)
 To install only the individual extensions you wish to have, change
 directories into each and use the Makefile.PL found there; for
   cd Bio/Ext/Align
   perl Makefile.PL
   make test (should print out alignment on STDERR)
   make install (probably need root permissions).

o Notes for Bio::Ext::Align

 Although these extensions can be called by themselves, they really
 need the main bioperl distribution to drive them. The modules which do
 this are
   Bio::Tools::pSW - makes Smith-Waterman alignments for DNA
   Bio::Tolls::dpAlign - makes Smith-Waterman alignments for proteins
   Bio::SearchDist - deals with EVD fitting of extreme value
 For more information on how to use these modules, read their own
 documentation (perldoc Bio::Tools::pSW ...)

o Notes for Bio::SeqIO::staden::read

 This extension needs the rest of the main bioperl distribution to
 function properly.  It is only useful as a helper module for the SeqIO
 system to read sequence trace files handled by the Staden package's
 io_lib "read" library.  You should have this library installed prior
 to installing Bio::SeqIO::staden::read, it's currently available at:
 Many users have noted that the io_lib install process often forgets to
 install the "os.h" file along with the rest of the include files; you
 may have to do this manually.
 The bioperl-ext make process will prompt you for the LIB and INCLUDE
 locations (usually /usr/local/lib and usr/local/include/io_lib,
 respectively) of the io_lib "libread" library and Read.h header files,
 after trying to automatically find them.  You may also specify these
 via the environment variables "IOLIB_LIB" and "IOLIB_INC", or via
 identically named options to perl Makefile.PL:
   perl Makefile.PL IOLIB_LIB=/opt/lib IOLIB_INC=/opt/include/io_lib
 Ignore any warnings about these options being unknown to MakeMaker.
 A failed compilation is most likely due to an incomplete io_lib
 installation; make sure that all the required io_lib ".h" files are in

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