AlignAid AlignAid is a Perl module that easily run sequence alignments locally or on a cluster.
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Perl module sequence sequence alignments cluster alignments AlignAid alignments

AlignAid Description

AlignAid is a Perl module that easily run sequence alignments locally or on a cluster. AlignAid is a Perl module that easily run sequence alignments locally or on a cluster.SYNOPSIS use AlignAid; # create an AlignAid object # a single, locally run blast job is the default my $job = AlignAid->new( db => 'my_blast_db', dir => $dir, fasta => 'my_query.fa', prog_args => 'V=20 -nonnegok' ); # run the job on the current host my $return_value = $job->submit(outfile => 'my_results.out'); # create an AlignAid cross_match object # specify the alignment program and the queue to override the defaults my $job2 = AlignAid->new( program => 'cross_match', db => 'my_db.fa', dir => $dir, fasta => 'my_query_seqs.fa', queue => 'LSF'); # submit the cross_match jobs to an LSF queue (of compute nodes) my $return_value2 = $job2->submit(outfile => 'my_output'); # kill the queued jobs my $return_value3 = $job2->kill_all;AlignAid is designed to make it easy to run the sequence alignment programs Blast and cross_match. AlignAid can accept a large number of query sequences. If a compute cluster queue such as LSF or PBS is available, AlignAid can automatically split the queries into multiple queue jobs.Likewise, if you want to run the alignments locally on a single host, a single change is all that is necessary -- AlignAid will take care of how to invoke the alignment programs and manage the output.AlignAid also has rudimentary support for LSF queue job control; it is possible to kill jobs through AlignAid's interface.What's New in This Release:· Perl

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