Bio::Tools::Run::Alignment::Clustalw - Object for the calculation of a multiple sequence alignment from a set of unaligned sequences or alignments using the Clustalw program # Build a clustalw alignment factory @params = ('ktuple' => 2, 'matrix' => 'BLOSUM'); $factory = Bio::Tools::Run::Alignment::Clustalw->new(@params); # Pass the factory a list of sequences to be aligned. $inputfilename = 't/data/cysprot.fa'; $aln = $factory->align($inputfilename); # $aln is a SimpleAlign object. # or $seq_array_ref = \@seq_array; # where @seq_array is an array of Bio::Seq objects $aln = $factory->align($seq_array_ref); # Or one can pass the factory a pair of (sub)alignments #to be aligned against each other, e.g.: $aln = $factory->profile_align($aln1,$aln2); # where $aln1 and $aln2 are Bio::SimpleAlign objects. # Or one can pass the factory an alignment and one or more unaligned # sequences to be added to the alignment. For example: $aln = $factory->profile_align($aln1,$seq); # $seq is a Bio::Seq object. # There are various additional options and input formats available. # See the DESCRIPTION section that follows for additional details. Note: this DESCRIPTION only documents the (Bio)perl interface to Clustalw. Clustalw, itself, is a large & complex program - for more information regarding clustalw, please see the clustalw documentation which accompanies the clustalw distribution. Clustalw is available from (among others) ftp://ftp.ebi.ac.uk/pub/software/. Clustalw.pm has been tested so far only under Linux. I expect that it should also work under other Unix systems. However, since the module is currently implemented using (unix) system calls, extensive modification may be necessary before Clustalw.pm would work under non-Unix operating systems (eg Windows, MacOS). Clustalw.pm has only been tested using version 1.8 of clustalw. Compatibility with earlier versions of the clustalw program is currently unknown. Before running Clustalw successfully it will be necessary: to install clustalw on your system, to edit the variable $clustdir in Clustalw.pm to point to the clustalw program, and to ensure that users have execute privilieges for the clustalw program.

Helping the module find your executable
You will need to enable Clustalw to find the clustalw program. This can be done in (at least) three ways: 1. Make sure the clustalw executable is in your path so that which clustalw returns a clustalw executable on your system. 2. Define an environmental variable CLUSTALDIR which is a directory which contains the 'clustalw' application: In bash export CLUSTALDIR=/home/username/clustalw1.8 In csh/tcsh setenv CLUSTALDIR /home/username/clustalw1.8 3. Include a definition of an environmental variable CLUSTALDIR in every script that will use this Clustalw wrapper module. BEGIN { $ENV{CLUSTALDIR} = '/home/username/clustalw1.8/' } use Bio::Tools::Run::Alignment::Clustalw; If you are running an application on a webserver make sure the webserver environment has the proper PATH set or use the options 2 or 3 to set the variables.

How it works
Bio::Tools::Run::Alignment::Clustalw is an object for performing a multiple sequence alignment from a set of unaligned sequences and/or sub-alignments by means of the clustalw program. Initially, a clustalw "factory object" is created. Optionally, the factory may be passed most of the parameters or switches of the clustalw program, e.g.: @params = ('ktuple' => 2, 'matrix' => 'BLOSUM'); $factory = Bio::Tools::Run::Alignment::Clustalw->new(@params); Any parameters not explicitly set will remain as the defaults of the clustalw program. Additional parameters and switches (not available in clustalw) may also be set. Currently, the only such parameter is "quiet", which when set to a non-zero value, suppresses clustalw terminal output. Not all clustalw parameters are supported at this stage. By default, Clustalw output is returned solely in a the form of a BioPerl Bio::SimpleAlign object which can then be printed and/or saved in multiple formats using the AlignIO.pm module. Optionally the raw clustalw output file can be saved if the calling script specifies an output file (with the clustalw parameter OUTFILE). Currently only the GCG-MSF output file formats is supported. Other parameters and features (such as those corresponding to tree production) have not been implemented yet in Perl format. Alignment parameters can be changed and/or examined at any time after the factory has been created. The program checks that any parameter/switch being set/read is valid. However, currently no additional checks are included to check that parameters are of the proper type (eg string or numeric) or that their values are within the proper range. As an example, to change the value of the clustalw parameter ktuple to 3 and subsequently to check its value one would write: $ktuple = 3; $factory->ktuple($ktuple); $get_ktuple = $factory->ktuple(); Once the factory has been created and the appropriate parameters set, one can call the method align() to align a set of unaligned sequences, or call profile_align() to add one or more sequences or a second alignment to an initial alignment. Input to align() may consist of a set of unaligned sequences in the form of the name of file containing the sequences. For example, $inputfilename = 't/data/cysprot.fa'; $aln = $factory->align($inputfilename); Alternately one can create an array of Bio::Seq objects somehow $str = Bio::SeqIO->new(-file=> 't/data/cysprot.fa', '-format' => 'Fasta'); @seq_array =(); while ( my $seq = $str->next_seq() ) {push (@seq_array, $seq) ;} and pass the factory a reference to that array $seq_array_ref = \@seq_array; $aln = $factory->align($seq_array_ref); In either case, align() returns a reference to a SimpleAlign object which can then be displayed, stored, or converted to a UnivAlign object for further manipulation. Once an initial alignment exists, one can pass the factory additional sequence(s) to be added (ie aligned) to the original alignment. The alignment can be passed as either an alignment file or a Bio:SimpleAlign object. The unaligned sequence(s) can be passed as a filename or as an array of BioPerl sequence objects or as a single BioPerl Seq object. For example (to add a single sequence to an alignment), $str = Bio::AlignIO->new(-file=> 't/data/cysprot1a.msf'); $aln = $str->next_aln(); $str1 = Bio::SeqIO->new(-file=> 't/data/cysprot1b.fa'); $seq = $str1->next_seq(); $aln = $factory->profile_align($aln,$seq); In either case, profile_align() returns a reference to a SimpleAlign object containing a new SimpleAlign object of the alignment with the additional sequence(s) added in. Finally one can pass the factory a pair of (sub)alignments to be aligned against each other. The alignments can be passed in the form of either a pair of alignment files or a pair of Bio:SimpleAlign objects. For example, $profile1 = 't/data/cysprot1a.msf'; $profile2 = 't/data/cysprot1b.msf'; $aln = $factory->profile_align($profile1,$profile2); or $str1 = Bio::AlignIO->new(-file=> 't/data/cysprot1a.msf'); $aln1 = $str1->next_aln(); $str2 = Bio::AlignIO->new(-file=> 't/data/cysprot1b.msf'); $aln2 = $str2->next_aln(); $aln = $factory->profile_align($aln1,$aln2); In either case, profile_align() returns a reference to a SimpleAlign object containing an (super)alignment of the two input alignments. For more examples of syntax and use of Clustalw, the user is encouraged to run the script Clustalw.t is the bioperl/t directory. Note: Clustalw is still under development. Various features of the clustalw program have not yet been implemented. If you would like that a specific clustalw feature be added to this perl interface, let me know. These can be specified as paramters when instantiating a new Clustalw object, or through get/set methods of the same name (lowercase).

KTUPLE
Title : KTUPLE Description : (optional) set the word size to be used in the alignment This is the size of exactly matching fragment that is used. INCREASE for speed (max= 2 for proteins; 4 for DNA), DECREASE for sensitivity. For longer sequences (e.g. >1000 residues) you may need to increase the default

TOPDIAGS
Title : TOPDIAGS Description : (optional) number of best diagonals to use The number of k-tuple matches on each diagonal (in an imaginary dot-matrix plot) is calculated. Only the best ones (with most matches) are used in the alignment. This parameter specifies how many. Decrease for speed; increase for sensitivity.

WINDOW
Title : WINDOW Description : (optional) window size This is the number of diagonals around each of the 'best' diagonals that will be used. Decrease for speed; increase for sensitivity.

PAIRGAP
Title : PAIRGAP Description : (optional) gap penalty for pairwise alignments This is a penalty for each gap in the fast alignments. It has little affect on the speed or sensitivity except for extreme values.

FIXEDGAP
Title : FIXEDGAP Description : (optional) fixed length gap penalty

FLOATGAP
Title : FLOATGAP Description : (optional) variable length gap penalty

MATRIX
Title : MATRIX Default : PAM100 for DNA - PAM250 for protein alignment Description : (optional) substitution matrix used in the multiple alignments. Depends on the version of clustalw as to what default matrix will be used PROTEIN WEIGHT MATRIX leads to a new menu where you are offered a choice of weight matrices. The default for proteins in version 1.8 is the PAM series derived by Gonnet and colleagues. Note, a series is used! The actual matrix that is used depends on how similar the sequences to be aligned at this alignment step are. Different matrices work differently at each evolutionary distance. DNA WEIGHT MATRIX leads to a new menu where a single matrix (not a series) can be selected. The default is the matrix used by BESTFIT for comparison of nucleic acid sequences.

TYPE
Title : TYPE Description : (optional) sequence type: protein or DNA. This allows you to explicitly overide the programs attempt at guessing the type of the sequence. It is only useful if you are using sequences with a VERY strange composition.

OUTPUT
Title : OUTPUT Description : (optional) clustalw supports GCG or PHYLIP or PIR or Clustal format. See the Bio::AlignIO modules for which formats are supported by bioperl.

OUTFILE
Title : OUTFILE Description : (optional) Name of clustalw output file. If not set module will erase output file. In any case alignment will be returned in the form of SimpleAlign objects

TRANSMIT
Title : TRANSMIT Description : (optional) transitions not weighted. The default is to weight transitions as more favourable than other mismatches in DNA alignments. This switch makes all nucleotide mismatches equally weighted.

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

Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: http://bugzilla.bioperl.org/ Email schattner@alum.mit.edu Jason Stajich jason@bioperl.org The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

program_name
Title : program_name Usage : $factory>program_name() Function: holds the program name Returns: string Args : None

program_dir
Title : program_dir Usage : $factory->program_dir(@params) Function: returns the program directory, obtiained from ENV variable. Returns: string Args :

version
Title : version Usage : exit if $prog->version() < 1.8 Function: Determine the version number of the program Example : Returns : float or undef Args : none

align
Title : align Usage : $inputfilename = 't/data/cysprot.fa'; $aln = $factory->align($inputfilename); or $seq_array_ref = \@seq_array; @seq_array is array of Seq objs $aln = $factory->align($seq_array_ref); Function: Perform a multiple sequence alignment Example : Returns : Reference to a SimpleAlign object containing the sequence alignment. Args : Name of a file containing a set of unaligned fasta sequences or else an array of references to Bio::Seq objects. Throws an exception if argument is not either a string (eg a filename) or a reference to an array of Bio::Seq objects. If argument is string, throws exception if file corresponding to string name can not be found. If argument is Bio::Seq array, throws exception if less than two sequence objects are in array.

profile_align
Title : profile_align Usage : Function: Perform an alignment of 2 (sub)alignments Example : Returns : Reference to a SimpleAlign object containing the (super)alignment. Args : Names of 2 files containing the subalignments or references to 2 Bio::SimpleAlign objects. Throws an exception if arguments are not either strings (eg filenames) or references to SimpleAlign objects.

tree
Title : tree Usage : @params = ('bootstrap' => 1000, 'tossgaps' => 1, 'kimura' => 1, 'seed' => 121, 'bootlabels'=> 'nodes', 'quiet' => 1); $factory = Bio::Tools::Run::Alignment::Clustalw->new(@params); $tree_obj = $factory->tree($aln_obj); or $tree_obj = $factory->tree($treefilename); Function: Returns : Bio::TreeIO object Args :

_run
Title : _run Usage : Internal function, not to be called directly Function: makes actual system call to clustalw program Example : Returns : nothing; clustalw output is written to a temporary file Args : Name of a file containing a set of unaligned fasta sequences and hash of parameters to be passed to clustalw

_setinput()
Title : _setinput Usage : Internal function, not to be called directly Function: Create input file for clustalw program Example : Returns : name of file containing clustalw data input Args : Seq or Align object reference or input file name

_setparams()
Title : _setparams Usage : Internal function, not to be called directly Function: Create parameter inputs for clustalw program Example : Returns : parameter string to be passed to clustalw during align or profile_align Args : name of calling object