AlignAid version 0.0.2 AlignAid is a simple module which makes it easy to run sequence alignment programs either locally or on a queue-based compute cluster. The user specifies which alignment program to use, the queries and the database, and what compute resources are available, and AlignAid takes care of the rest. This capability is especially useful when you need to perform a large number of alignments and have a compute cluster queue available; AlignAid will split the task into multiple queue jobs, track their completion, and collate the results. The straightforward interface also comes in handy when you want to program to adjust to the compute resources available to it. Using AlignAid, the program could check for a queue and use it if available or run the alignments locally if not. For complete instructions, see the documentation for AlignAid by typing: perldoc AlignAid INSTALLATION To install this module, run the following commands: perl Makefile.PL make make test make install Alternatively, to install with Module::Build, you can use the following commands: perl Build.PL ./Build ./Build test ./Build install DEPENDENCIES Bio::SeqIO - part of BioPerl, available at bioperl.org version - available from CPAN PP - This is an optional dependency, needed if you want to submit jobs to a compute cluster queueing system like LSF. BPdeluxe 1.0 - This is an optional dependency, needed only if you want to use the validate_blasts() method. Available from Jarret Glasscock (glasscock_cpan at mac dot com). COPYRIGHT AND LICENCE Copyright (C) 2006, Dave Messina . This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself.