Bio::Tools::Run::Alignment Clustalw
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Summary
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
Package variables
No package variables defined.
Included modules
Bio::AlignIO
Bio::Root::IO
Bio::Seq
Bio::SeqIO
Bio::SimpleAlign
Bio::TreeIO
Inherit
Bio::Root::Root Bio::Tools::Run::WrapperBase
Synopsis
  #  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. # Get a tree of the sequences $tree = $factory->tree(\@seq_array); # Get both an alignment and a tree ($aln, $tree) = $factory->run(\@seq_array); # Do a footprinting analysis on the supplied sequences, getting back the # most conserved sub-alignments my @results = $factory->footprint(\@seq_array); foreach my $result (@results) { print $result->consensus_string, "\n"; } # There are various additional options and input formats available. # See the DESCRIPTION section that follows for additional details.
Description
Note: this DESCRIPTION only documents the Bioperl 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
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, and to ensure that users have execute privileges for
the clustalw program. 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, e.g.: 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. 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
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.
Not all parameters and features have 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 used (see Bio::SimpleAlign).
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 look at the script Clustalw.t in the 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 contact bioperl-l@bioperl.org.
These can be specified as paramters when instantiating a new Clustalw
object, or through get/set methods of the same name (lowercase).
Methods
program_nameDescriptionCode
program_dirDescriptionCode
new
No description
Code
versionDescriptionCode
runDescriptionCode
alignDescriptionCode
profile_alignDescriptionCode
add_sequencesDescriptionCode
treeDescriptionCode
footprintDescriptionCode
_runDescriptionCode
_get_tree
No description
Code
_setinputDescriptionCode
_setparamsDescriptionCode
Methods description
program_namecode    nextTop
 Title   : program_name
Usage : $factory>program_name()
Function: holds the program name
Returns: string
Args : None
program_dircodeprevnextTop
 Title   : program_dir
Usage : $factory->program_dir(@params)
Function: returns the program directory, obtained from ENV variable.
Returns: string
Args :
versioncodeprevnextTop
 Title   : version
Usage : exit if $prog->version() < 1.8
Function: Determine the version number of the program
Example :
Returns : float or undef
Args : none
runcodeprevnextTop
 Title   : run
Usage : ($aln, $tree) = $factory->run($inputfilename);
($aln, $tree) = $factory->run($seq_array_ref);
Function: Perform a multiple sequence alignment, generating a tree at the same
time. (Like align() and tree() combined.)
Returns : A SimpleAlign object containing the sequence alignment and a
Bio::Tree::Tree object with the tree relating the sequences.
Args : Name of a file containing a set of unaligned fasta sequences
or else an array of references to Bio::Seq objects.
aligncodeprevnextTop
 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
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_aligncodeprevnextTop
 Title   : profile_align
Usage : $aln = $factory->profile_align(@simple_aligns);
or
$aln = $factory->profile_align(@subalignment_filenames);
Function: Perform an alignment of 2 (sub)alignments
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.
add_sequencescodeprevnextTop
 Title   : add_sequences
Usage :
Function: Align and add sequences into an alignment
Example :
Returns : Reference to a SimpleAlign object containing the (super)alignment.
Args : Names of 2 files, the first one containing an alignment and the second one containing sequences to be added
or references to 2 Bio::SimpleAlign objects.
Throws an exception if arguments are not either strings (eg filenames)
or references to SimpleAlign objects.
treecodeprevnextTop
 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: Retrieve a tree corresponding to the input
Returns : Bio::TreeIO object
Args : Bio::SimpleAlign or filename of a tree
footprintcodeprevnextTop
 Title   : footprint
Usage : @alns = $factory->footprint($treefilename, $window_size, $diff);
@alns = $factory->footprint($seqs_array_ref);
Function: Aligns all the supplied sequences and slices out of the alignment
those regions along a sliding window who's tree length differs
significantly from the total average tree length.
Returns : list of Bio::SimpleAlign objects
Args : first argument as per run(), optional second argument to specify
the size of the sliding window (default 5 bp) and optional third
argument to specify the % difference from the total tree length
needed for a window to be considered a footprint (default 33%).
_runcodeprevnextTop
 Title   : _run
Usage : Internal function, not to be called directly
Function: makes actual system call to clustalw program
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()codeprevnextTop
 Title   : _setinput
Usage : Internal function, not to be called directly
Function: Create input file for clustalw program
Returns : name of file containing clustalw data input
Args : Seq or Align object reference or input file name
_setparams()codeprevnextTop
 Title   : _setparams
Usage : Internal function, not to be called directly
Function: Create parameter inputs for clustalw program
Returns : parameter string to be passed to clustalw
during align or profile_align
Args : name of calling object
Methods code
program_namedescriptionprevnextTop
sub program_name {
  return $PROGRAM_NAME;
}
program_dirdescriptionprevnextTop
sub program_dir {
  return $PROGRAM_DIR;
}
newdescriptionprevnextTop
sub new {
    my ($class,@args) = @_;
    my $self = $class->SUPER::new(@args);

    $self->_set_from_args(\@args, -methods => [@CLUSTALW_PARAMS,
                                               @CLUSTALW_SWITCHES,
                                               @OTHER_SWITCHES],
                                  -create => 1);
    
    return $self;
}
versiondescriptionprevnextTop
sub version {
    my ($self) = @_;

    return undef unless $self->executable;
    my $prog = $self->executable;
    my $string = `$prog --` ;
    $string =~ /\(?([\d.]+)\)?/xms;
    return $1 || undef;
}
rundescriptionprevnextTop
sub run {
    my ($self,$input) = @_;
    my ($temp,$infilename, $seq);
    my ($attr, $value, $switch);
    
    $self->io->_io_cleanup();
    # Create input file pointer
$infilename = $self->_setinput($input); $self->throw("Bad input data (sequences need an id) or less than 2 sequences in $input!") unless $infilename; # Create parameter string to pass to clustalw program
my $param_string = $self->_setparams(); # run clustalw
return $self->_run('both', $infilename, $param_string);
}
aligndescriptionprevnextTop
sub align {
    my ($self,$input) = @_;
    
    $self->io->_io_cleanup();
    
    # Create input file pointer
my $infilename = $self->_setinput($input); $self->throw("Bad input data (sequences need an id ) or less than 2 sequences in $input !") unless $infilename; # Create parameter string to pass to clustalw program
my $param_string = $self->_setparams(); # run clustalw
my $aln = $self->_run('align', $infilename, $param_string);
}
profile_aligndescriptionprevnextTop
sub profile_align {
    my ($self,$input1,$input2) = @_;
    
    $self->io->_io_cleanup();
    
    # Create input file pointer
my $infilename1 = $self->_setinput($input1, 1); my $infilename2 = $self->_setinput($input2, 2); if (!$infilename1 || !$infilename2) {$self->throw("Bad input data: $input1 or $input2 !");} unless ( -e $infilename1 and -e $infilename2) {$self->throw("Bad input file: $input1 or $input2 !");} # Create parameter string to pass to clustalw program
my $param_string = $self->_setparams(); # run clustalw
my $aln = $self->_run('profile-aln', $infilename1, $infilename2, $param_string);
}
add_sequencesdescriptionprevnextTop
sub add_sequences {
    my ($self,$input1,$input2) = @_;
    my ($temp,$infilename1,$infilename2,$input,$seq);
    
    $self->io->_io_cleanup();
    # Create input file pointer
$infilename1 = $self->_setinput($input1,1); $infilename2 = $self->_setinput($input2,2); if (!$infilename1 || !$infilename2) {$self->throw("Bad input data: $input1 or $input2 !");} unless ( -e $infilename1 and -e $infilename2) {$self->throw("Bad input file: $input1 or $input2 !");} # Create parameter string to pass to clustalw program
my $param_string = $self->_setparams(); # run clustalw
my $aln = $self->_run('add_sequences', $infilename1, $infilename2, $param_string);
}
treedescriptionprevnextTop
sub tree {
    my ($self,$input) = @_;
    
    $self->io->_io_cleanup();
    
    # Create input file pointer
my $infilename = $self->_setinput($input); if (!$infilename) {$self->throw("Bad input data (sequences need an id ) or less than 2 sequences in $input !");} # Create parameter string to pass to clustalw program
my $param_string = $self->_setparams(); # run clustalw
my $tree = $self->_run('tree', $infilename, $param_string);
}
footprintdescriptionprevnextTop
sub footprint {
    my ($self, $in, $slice_size, $deviate) = @_;
    
    my ($simplealn, $tree) = $self->run($in);
    
    # total tree length?
my $total_length = $tree->total_branch_length; # tree length along sliding window, picking regions that significantly
# deviate from the average tree length
$slice_size ||= 5; $deviate ||= 33; my $threshold = $total_length - (($total_length / 100) * $deviate);
my $length = $simplealn->length; my $below = 0; my $found_minima = 0; my $minima = [$threshold, '']; my @results; for my $i (1..($length - $slice_size + 1)) { my $slice = $simplealn->slice($i, ($i + $slice_size - 1), 1); my $tree = $self->tree($slice); my $slice_length = $tree->total_branch_length; $slice_length <= $threshold ? ($below = 1) : ($below = 0); if ($below) { unless ($found_minima) { if ($slice_length < ${$minima}[0]) { $minima = [$slice_length, $slice]; } else { push(@results, ${$minima}[1]); $minima = [$threshold, '']; $found_minima = 1; } } } else { $found_minima = 0; } } return @results;
}
_rundescriptionprevnextTop
sub _run {
    my ($self, $command, $infile1, $infile2, $param_string) = @_;
    
    my ($instring, $tree);
    my $quiet = $self->quiet() || $self->verbose() < 0;
    
    if ($command =~ /align|both/) {
        if ($^O eq 'dec_osf') {
            $instring = $infile1;
            $command = '';
        }
        else { 
            $instring = " -infile=$infile1";
        }
        $param_string .= " $infile2";
    }
    
    if ($command =~ /profile/) {
        $instring =  "-profile1=$infile1  -profile2=$infile2";
    	chmod 0777, $infile1, $infile2;
    	$command = '-profile';
    }
    
    if ($command =~ /add_sequences/) {
      $instring =  "-profile1=$infile1  -profile2=$infile2";
      chmod 0777, $infile1,$infile2;
      $command = '-sequences';
    }

    if ($command =~ /tree/) {
    	if( $^O eq 'dec_osf' ) {
            $instring =  $infile1;
            $command = '';
        }
        else { 
            $instring = " $infile1";
        }
    	$param_string .= " $infile2";
        
    	$self->debug( "Program ".$self->executable."\n");
    	my $commandstring = $self->executable."$instring"."$param_string";
        $commandstring .= ' 1>/dev/null' if $quiet;
        $self->debug( "clustal command = $commandstring");
        
        my $status = system($commandstring);
        unless( $status == 0 ) {
            $self->warn( "Clustalw call ($commandstring) crashed: $?\n ");
            return undef;
        }
        
    	return $self->_get_tree($infile1, $param_string);
    }
    
    my $output = $self->output || 'gcg';
    $self->debug( "Program ".$self->executable."\n");
    my $commandstring = $self->executable." $command"." $instring"." -output=$output". " $param_string";
    $self->debug( "clustal command = $commandstring");
    
    open(my $pipe, "$commandstring |") || $self->throw("ClustalW call ($commandstring) failed to start: $? | $!");
    my $score;
    while (<$pipe>) {
        print unless $quiet;
        # Kevin Brown suggested the following regex, though it matches multiple
# times: we pick up the last one
$score = $1 if ($_ =~ /Score:(\d+)/); # This one is printed at the end and seems the most appropriate to pick
# up; we include the above regex incase 'Alignment Score' isn't given
$score = $1 if ($_ =~ /Alignment Score (-?\d+)/); } close($pipe) || ($self->throw("ClustalW call ($commandstring) crashed: $?")); my $outfile = $self->outfile(); # retrieve alignment (Note: MSF format for AlignIO = GCG format of clustalw)
my $format = $output =~ /gcg/i ? 'msf' : $output; if ($format =~ /clustal/i) { $format = 'clustalw'; # force clustalw incase 'clustal' is requested
} my $in = Bio::AlignIO->new(-file => $outfile, -format=> $format); my $aln = $in->next_aln(); $in->close; $aln->score($score); if ($command eq 'both') { $tree = $self->_get_tree($infile1, $param_string); } # Clean up the temporary files created along the way...
# Replace file suffix with dnd to find name of dendrogram file(s) to delete
unless ( $self->save_tempfiles ) { foreach my $f ($infile1, $infile2) { $f =~ s/\.[^\.]*$// ; unlink $f .'.dnd' if ($f ne ''); } } if ($command eq 'both') { return ($aln, $tree); } return $aln;
}
_get_treedescriptionprevnextTop
sub _get_tree {
    my ($self, $treefile, $param_string) = @_;
    
    $treefile =~ s/\.[^\.]*$// ;
    
    if ($param_string =~ /-bootstrap/) {
        $treefile .= '.phb';
    }
    elsif ($param_string =~ /-tree/) {
        $treefile .= '.ph';
    }
    else {
        $treefile .= '.dnd';
    }
    
    my $in = Bio::TreeIO->new('-file'  => $treefile,
                             '-format'=> 'newick');
    
    my $tree = $in->next_tree;
    unless ( $self->save_tempfiles ) {
        foreach my $f ( $treefile ) {
            unlink $f if( $f ne '' );
        }
    }
    
    return $tree;
}
_setinputdescriptionprevnextTop
sub _setinput {
    my ($self, $input, $suffix) = @_;
    my ($infilename, $seq, $temp, $tfh);
    
    # suffix is used to distinguish alignment files If $input is not a
# reference it better be the name of a file with the sequence/
# alignment data...
unless (ref $input) { # check that file exists or throw
$infilename = $input; return unless -e $input; return $infilename; } # $input may be an array of BioSeq objects...
if (ref($input) eq "ARRAY") { # Open temporary file for both reading & writing of BioSeq array
($tfh,$infilename) = $self->io->tempfile(-dir=>$self->tempdir); $temp = Bio::SeqIO->new('-fh'=>$tfh, '-format' =>'Fasta'); # Need at least 2 seqs for alignment
return unless (scalar(@$input) > 1); foreach $seq (@$input) { return unless (defined $seq && $seq->isa("Bio::PrimarySeqI") and $seq->id()); $temp->write_seq($seq); } $temp->close(); close($tfh); undef $tfh; return $infilename; } # $input may be a SimpleAlign object.
elsif (ref($input) eq "Bio::SimpleAlign") { # Open temporary file for both reading & writing of SimpleAlign object
($tfh,$infilename) = $self->io->tempfile(-dir=>$self->tempdir); $temp = Bio::AlignIO->new('-fh'=> $tfh, '-format' => 'fasta'); $temp->write_aln($input); close($tfh); undef $tfh; return $infilename; } # or $input may be a single BioSeq object (to be added to a previous alignment)
elsif (ref($input) && $input->isa("Bio::PrimarySeqI") && $suffix==2) { # Open temporary file for both reading & writing of BioSeq object
($tfh,$infilename) = $self->io->tempfile(); $temp = Bio::SeqIO->new(-fh=> $tfh, '-format' =>'Fasta'); $temp->write_seq($input); close($tfh); undef $tfh; return $infilename; } return;
}
_setparamsdescriptionprevnextTop
sub _setparams {
    my $self = shift;
    
    my $param_string = $self->SUPER::_setparams(-params =>\@ CLUSTALW_PARAMS,
                                                -switches =>\@ CLUSTALW_SWITCHES,
                                                -dash => 1,
                                                -lc => 1,
                                                -join => '=');
    
    # Set default output file if no explicit output file selected
unless ($param_string =~ /outfile/) { my ($tfh, $outfile) = $self->io->tempfile(-dir => $self->tempdir()); close($tfh); undef $tfh; $self->outfile($outfile); $param_string .= " -outfile=$outfile" ; } $param_string .= ' 2>&1'; return $param_string; } 1;
}
General documentation
PARAMETER FOR ALIGNMENT COMPUTATIONTop
KTUPLETop
 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
TOPDIAGSTop
 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.
WINDOWTop
 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.
PAIRGAPTop
 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.
FIXEDGAPTop
 Title       : FIXEDGAP
Description : (optional) fixed length gap penalty
FLOATGAPTop
 Title       : FLOATGAP
Description : (optional) variable length gap penalty
MATRIXTop
 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.
TYPETop
 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.
OUTPUTTop
 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.
OUTFILETop
 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
TRANSMITTop
 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.
FEEDBACKTop
Mailing ListsTop
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://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support Top
 
Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
Reporting BugsTop
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.open-bio.org/
AUTHOR - Peter SchattnerTop
Email schattner@alum.mit.edu
CONTRIBUTORSTop
Jason Stajich jason-AT-bioperl_DOT_org
Sendu Bala bix@sendu.me.uk
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _