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.IX Title "Bio::Tools::Run::Phylo::QuickTree 3pm"
.TH Bio::Tools::Run::Phylo::QuickTree 3pm "2023-01-22" "perl v5.36.0" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.SH "NAME"
Bio::Tools::Run::Phylo::QuickTree \- Wrapper for rapid reconstruction of
                                    phylogenies using QuickTree
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 1
\&  use Bio::Tools::Run::Phylo::QuickTree;
\&
\&  #  Make a QuickTree factory
\&  @params = ();
\&  $factory = Bio::Tools::Run::Phylo::QuickTree\->new(@params);
\&
\&  #  Pass the factory an alignment      
\&  $inputfilename = \*(Aqt/data/cysprot.stockholm\*(Aq;
\&  $tree = $factory\->run($inputfilename); # $tree is a Bio::Tree::Tree object.
\&  # or get a Bio::Align::AlignI (SimpleAlign) object from somewhere
\&  $tree = $factory\->run($aln);
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
This is a wrapper for running the QuickTree application by Kevin Howe. You
can download it here: http://www.sanger.ac.uk/Software/analysis/quicktree/
.PP
Currently only input with alignments and output of trees is supported. (Ie.
no support for distance matrix in/out.)
.PP
You will need to enable this QuickTree wrapper to find the quicktree program.
This can be done in (at least) three ways:
.PP
.Vb 4
\& 1. Make sure the QuickTree executable is in your path.
\& 2. Define an environmental variable QUICKTREEDIR which is a 
\&    directory which contains the \*(Aqquicktree\*(Aq application:
\&    In bash:
\&
\&    export QUICKTREEDIR=/home/username/quicktree_1.1/bin
\&
\&    In csh/tcsh:
\&
\&    setenv QUICKTREEDIR /home/username/quicktree_1.1/bin
\&
\& 3. Include a definition of an environmental variable QUICKTREEDIR in
\&    every script that will use this QuickTree wrapper module, e.g.:
\&
\&    BEGIN { $ENV{QUICKTREEDIR} = \*(Aq/home/username/quicktree_1.1/bin\*(Aq }
\&    use Bio::Tools::Run::Phylo::QuickTree;
.Ve
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "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.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS "Support"
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
\&\fIbioperl\-l@bioperl.org\fR
.PP
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.
.SS "Reporting Bugs"
.IX Subsection "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:
.PP
.Vb 1
\&  http://redmine.open\-bio.org/projects/bioperl/
.Ve
.SH "AUTHOR \- Sendu Bala"
.IX Header "AUTHOR - Sendu Bala"
Email bix@sendu.me.uk
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
.SS "program_name"
.IX Subsection "program_name"
.Vb 5
\& Title   : program_name
\& Usage   : $factory>program_name()
\& Function: holds the program name
\& Returns : string
\& Args    : None
.Ve
.SS "program_dir"
.IX Subsection "program_dir"
.Vb 5
\& Title   : program_dir
\& Usage   : $factory\->program_dir(@params)
\& Function: returns the program directory, obtained from ENV variable.
\& Returns : string
\& Args    : None
.Ve
.SS "new"
.IX Subsection "new"
.Vb 9
\& Title   : new
\& Usage   : $factory = Bio::Tools::Run::Phylo::QuickTree\->new(@params)
\& Function: creates a new QuickTree factory
\& Returns : Bio::Tools::Run::Phylo::QuickTree
\& Args    : Optionally, provide any of the following (default in []):
\&           \-upgma  => boolean # Use the UPGMA method to construct the tree [0]
\&           \-kimura => boolean # Use the kimura translation for pairwise
\&                              # distances [0]
\&           \-boot   => int     # Calculate bootstrap values with n iterations [0]
.Ve
.SS "upgma"
.IX Subsection "upgma"
.Vb 5
\& Title   : upgma
\& Usage   : $factory\->upgma(1);
\& Function: Choose to use the UPGMA method to construct the tree.
\& Returns : boolean (default 0)
\& Args    : None to get, boolean to set.
.Ve
.SS "kimura"
.IX Subsection "kimura"
.Vb 5
\& Title   : kimura
\& Usage   : $factory\->kimura(1);
\& Function: Choose to use the kimura translation for pairwise distances.
\& Returns : boolean (default 0)
\& Args    : None to get, boolean to set.
.Ve
.SS "boot"
.IX Subsection "boot"
.Vb 6
\& Title   : boot
\& Usage   : $factory\->boot(100);
\& Function: Choose to calculate bootstrap values with the supplied number of
\&           iterations.
\& Returns : int (default 0)
\& Args    : None to get, int to set.
.Ve
.SS "run"
.IX Subsection "run"
.Vb 7
\& Title   : run
\& Usage   : $factory\->run($stockholm_file);
\&           $factory\->run($align_object);
\& Function: Runs QuickTree to generate a tree 
\& Returns : Bio::Tree::Tree object
\& Args    : file name for your input alignment in stockholm format, OR
\&           Bio::Align::AlignI compliant object (eg. Bio::SimpleAlign).
.Ve
.SS "_setparams"
.IX Subsection "_setparams"
.Vb 5
\& Title   : _setparams
\& Usage   : Internal function, not to be called directly
\& Function: Creates a string of params to be used in the command string
\& Returns : string of params
\& Args    : none
.Ve
.SS "_writeAlignFile"
.IX Subsection "_writeAlignFile"
.Vb 5
\& Title   : _writeAlignFile
\& Usage   : obj\->_writeAlignFile($seq)
\& Function: Internal(not to be used directly)
\& Returns : filename
\& Args    : Bio::Align::AlignI
.Ve