Bio::Tools::Run::Alignment::Lagan - Object for the local execution of the LAGAN suite of tools (including MLAGAN for multiple sequence alignments) use Bio::Tools::Run::Alignment::Lagan; @params = ('chaos' => "The contents of this string will be passed as args to chaos", #Read you chaos README file for more info/This functionality #has not been tested and will be integrated in future versions. 'order' => "\"-gs -7 -gc -2 -mt 2 -ms -1\"", #Where gap start penalty of- 7, gap continue of -2, match of 2, #and mismatch of -1. 'recurse' => "\"(12,25),(7,25),(4,30)"\", #A list of (wordlength,score cutoff) pairs to be used in the #recursive anchoring 'tree' => "\"(sample1 (sample2 sample3))"\", #Used by mlagan / tree can also be passed when calling mlagan directly #SCORING PARAMETERS FOR MLAGAN: 'match' => 12, 'mismatch' => -8, 'gapstart' => -50, 'gapend' => -50, 'gapcont' => -2, ); To run mlagan/lagan, the executables "mlagan" and "lagan.pl" must be in your path or you must have an environment variable that points to the executable directory "LAGANDIR=/opt/lagan_executables/" All lagan and mlagan parameters listed in their Readmes can be set except for the mfa flag which has been turned on by default to prevent parsing of the alignment format. TO USE LAGAN: my $lagan = new Bio::Tools::Run::Alignment::Lagan(@params); my $report_out = $lagan->lagan($seq1, $seq2); A SimpleAlign object is returned. TO USE MLAGAN: my $lagan = new Bio::Tools::Run::Alignment::Lagan(); my $tree = "(($seqname1 $seqname2) $seqname3)"; my @sequence_objs; #an array of bioperl Seq objects ##If you use an unblessed seq array my $seq_ref = \@sequence_objs; bless $seq_ref, "ARRAY"; my $report_out = $lagan->mlagan($seq_ref, $tree); A SimpleAlign object is returned Only basic mlagan/lagan functionality has been implemented due to the iterative development of their project. Future maintenance upgrades will include enhanced features and scoring.

Mailing Lists
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/MailList.shtml - About the mailing lists

Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: http://bugzilla.bioperl.org/ Email smontgom@bcgsc.bc.ca Genome Sciences Centre in beautiful Vancouver, British Columbia CANADA MLagan/Lagan is the hard work of Michael Brudno et al. The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

lagan
Runs the Lagan pairwise alignment algorithm Inputs should be two PrimarySeq objects. Returns an SimpleAlign object / preloaded with the tmp file of the Lagan multifasta output.

mlagan
Runs the Mlagan multiple sequence alignment algorithm Inputs should be an Array of Primary Seq objects and a Phylogenetic Tree in String format Returns an SimpleAlign object / preloaded with the tmp file of the Mlagan multifasta output.

_setinput
Title : _setinput Usage : Internal function, not to be called directly Function: Create input file(s) for Lagan executables Returns : name of files containing Lagan data input / or array of files and phylo tree for Mlagan data input

_generic_lagan
Title : _generic_lagan Usage : internal function not called directly Returns : SimpleAlign object

_setparams
Title : _setparams Usage : Internal function, not to be called directly Function: Create parameter inputs for (m)Lagan program Returns : parameter string to be passed to Lagan Args : Reference to calling object and name of (m)Lagan executable

_runlagan
Title : _runlagan Usage : Internal function, not to be called directly Function: makes actual system call to (m)Lagan program Example : Returns : Report object in the SimpleAlign object

executable
Title : executable Usage : my $exe = $lagan->executable('mlagan'); Function: Finds the full path to the 'lagan' executable Returns : string representing the full path to the exe Args : [optional] name of executable to set path to [optional] boolean flag whether or not warn when exe is not found Thanks to Jason Stajich for providing the framework for this subroutine

program_path
Title : program_path Usage : my $path = $lagan->program_path(); Function: Builds path for executable Returns : string representing the full path to the exe Thanks to Jason Stajich for providing the framework for this subroutine

program_dir
Title : program_dir Usage : my $dir = $lagan->program_dir(); Function: Abstract get method for dir of program. To be implemented by wrapper. Returns : string representing program directory Thanks to Jason Stajich for providing the framework for this subroutine