You can check if you have them installed in your machine with:

> perl -e 1 -M<module>

It will return an error message if it isn't installed.

Use the commands below to check if they are installed:

perl -e 1 -MBio::SeqIO

perl -e 1 -MBio::AlignIO

perl -e 1 -MCwd

perl -e 1 -MFile::chdir

perl -e 1 -MFile::Copy

perl -e 1 -MPOSIX

You can install these modules through the CPAN, or manually download

(http://search.cpan.org/) and compile them. To use CPAN, you can do by

writing:

> perl -MCPAN -e 'install "<module>"'

Use the commands below to install with CPAN:

perl -MCPAN -e 'install "Bio::SeqIO"'

perl -MCPAN -e 'install "Bio::AlignIO"'

perl -MCPAN -e 'install "Cwd"'

perl -MCPAN -e 'install "File::chdir"'

perl -MCPAN -e 'install "File::Copy"'

perl -MCPAN -e 'install "POSIX"' 

To install manually, search for the most recent version of these modules and,

for each, download and type the following (should work most of the time, except

for BioPerl):

> tar -zxvf <module.tar.gz>

> perl Makefile.PL

> make

> make test

> make install