.\" Automatically generated by Pod::Man 4.14 (Pod::Simple 3.43)
.\"
.\" Standard preamble:
.\" ========================================================================
.de Sp \" Vertical space (when we can't use .PP)
.if t .sp .5v
.if n .sp
..
.de Vb \" Begin verbatim text
.ft CW
.nf
.ne \\$1
..
.de Ve \" End verbatim text
.ft R
.fi
..
.\" Set up some character translations and predefined strings.  \*(-- will
.\" give an unbreakable dash, \*(PI will give pi, \*(L" will give a left
.\" double quote, and \*(R" will give a right double quote.  \*(C+ will
.\" give a nicer C++.  Capital omega is used to do unbreakable dashes and
.\" therefore won't be available.  \*(C` and \*(C' expand to `' in nroff,
.\" nothing in troff, for use with C<>.
.tr \(*W-
.ds C+ C\v'-.1v'\h'-1p'\s-2+\h'-1p'+\s0\v'.1v'\h'-1p'
.ie n \{\
.    ds -- \(*W-
.    ds PI pi
.    if (\n(.H=4u)&(1m=24u) .ds -- \(*W\h'-12u'\(*W\h'-12u'-\" diablo 10 pitch
.    if (\n(.H=4u)&(1m=20u) .ds -- \(*W\h'-12u'\(*W\h'-8u'-\"  diablo 12 pitch
.    ds L" ""
.    ds R" ""
.    ds C` ""
.    ds C' ""
'br\}
.el\{\
.    ds -- \|\(em\|
.    ds PI \(*p
.    ds L" ``
.    ds R" ''
.    ds C`
.    ds C'
'br\}
.\"
.\" Escape single quotes in literal strings from groff's Unicode transform.
.ie \n(.g .ds Aq \(aq
.el       .ds Aq '
.\"
.\" If the F register is >0, we'll generate index entries on stderr for
.\" titles (.TH), headers (.SH), subsections (.SS), items (.Ip), and index
.\" entries marked with X<> in POD.  Of course, you'll have to process the
.\" output yourself in some meaningful fashion.
.\"
.\" Avoid warning from groff about undefined register 'F'.
.de IX
..
.nr rF 0
.if \n(.g .if rF .nr rF 1
.if (\n(rF:(\n(.g==0)) \{\
.    if \nF \{\
.        de IX
.        tm Index:\\$1\t\\n%\t"\\$2"
..
.        if !\nF==2 \{\
.            nr % 0
.            nr F 2
.        \}
.    \}
.\}
.rr rF
.\"
.\" Accent mark definitions (@(#)ms.acc 1.5 88/02/08 SMI; from UCB 4.2).
.\" Fear.  Run.  Save yourself.  No user-serviceable parts.
.    \" fudge factors for nroff and troff
.if n \{\
.    ds #H 0
.    ds #V .8m
.    ds #F .3m
.    ds #[ \f1
.    ds #] \fP
.\}
.if t \{\
.    ds #H ((1u-(\\\\n(.fu%2u))*.13m)
.    ds #V .6m
.    ds #F 0
.    ds #[ \&
.    ds #] \&
.\}
.    \" simple accents for nroff and troff
.if n \{\
.    ds ' \&
.    ds ` \&
.    ds ^ \&
.    ds , \&
.    ds ~ ~
.    ds /
.\}
.if t \{\
.    ds ' \\k:\h'-(\\n(.wu*8/10-\*(#H)'\'\h"|\\n:u"
.    ds ` \\k:\h'-(\\n(.wu*8/10-\*(#H)'\`\h'|\\n:u'
.    ds ^ \\k:\h'-(\\n(.wu*10/11-\*(#H)'^\h'|\\n:u'
.    ds , \\k:\h'-(\\n(.wu*8/10)',\h'|\\n:u'
.    ds ~ \\k:\h'-(\\n(.wu-\*(#H-.1m)'~\h'|\\n:u'
.    ds / \\k:\h'-(\\n(.wu*8/10-\*(#H)'\z\(sl\h'|\\n:u'
.\}
.    \" troff and (daisy-wheel) nroff accents
.ds : \\k:\h'-(\\n(.wu*8/10-\*(#H+.1m+\*(#F)'\v'-\*(#V'\z.\h'.2m+\*(#F'.\h'|\\n:u'\v'\*(#V'
.ds 8 \h'\*(#H'\(*b\h'-\*(#H'
.ds o \\k:\h'-(\\n(.wu+\w'\(de'u-\*(#H)/2u'\v'-.3n'\*(#[\z\(de\v'.3n'\h'|\\n:u'\*(#]
.ds d- \h'\*(#H'\(pd\h'-\w'~'u'\v'-.25m'\f2\(hy\fP\v'.25m'\h'-\*(#H'
.ds D- D\\k:\h'-\w'D'u'\v'-.11m'\z\(hy\v'.11m'\h'|\\n:u'
.ds th \*(#[\v'.3m'\s+1I\s-1\v'-.3m'\h'-(\w'I'u*2/3)'\s-1o\s+1\*(#]
.ds Th \*(#[\s+2I\s-2\h'-\w'I'u*3/5'\v'-.3m'o\v'.3m'\*(#]
.ds ae a\h'-(\w'a'u*4/10)'e
.ds Ae A\h'-(\w'A'u*4/10)'E
.    \" corrections for vroff
.if v .ds ~ \\k:\h'-(\\n(.wu*9/10-\*(#H)'\s-2\u~\d\s+2\h'|\\n:u'
.if v .ds ^ \\k:\h'-(\\n(.wu*10/11-\*(#H)'\v'-.4m'^\v'.4m'\h'|\\n:u'
.    \" for low resolution devices (crt and lpr)
.if \n(.H>23 .if \n(.V>19 \
\{\
.    ds : e
.    ds 8 ss
.    ds o a
.    ds d- d\h'-1'\(ga
.    ds D- D\h'-1'\(hy
.    ds th \o'bp'
.    ds Th \o'LP'
.    ds ae ae
.    ds Ae AE
.\}
.rm #[ #] #H #V #F C
.\" ========================================================================
.\"
.IX Title "Bio::Tools::Run::Phylo::Raxml 3pm"
.TH Bio::Tools::Run::Phylo::Raxml 3pm "2023-01-22" "perl v5.36.0" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
.if n .ad l
.nh
.SH "NAME"
Bio::Tools::Run::Phylo::Raxml \- Bio::Tree getter from DNA alignment through raxml
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 2
\&  # Build a Raxml factory
\&  $factory = Bio::Tools::Run::Phylo::Raxml\->new(\-p  => 100);
\&
\&  # Get an alignment
\&  my $alignio = Bio::AlignIO\->new(
\&        \-format => \*(Aqfasta\*(Aq,
\&        \-file   => \*(Aq219877.cdna.fasta\*(Aq);
\&  my $alnobj = $alignio\->next_aln;
\&
\&  # Analyze the aligment and get a Tree
\&  my $tree = $factory\->run($alnobj);
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
Get a Bio::Tree object using raxml given a protein or \s-1DNA\s0 alignment.
.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 one
of the Bioperl mailing lists.  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
Do not contact the module maintainer directly. Many experienced experts 
at bioperl-l 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
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 \-  Brian Osborne"
.IX Header "AUTHOR - Brian Osborne"
Email briano@bioteam.net
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
.SS "new"
.IX Subsection "new"
.Vb 5
\& Title   : new
\& Usage   : my $treebuilder = Bio::Tools::Run::Phylo::Raxml\->new();
\& Function: Constructor
\& Returns : Bio::Tools::Run::Phylo::Raxml
\& Args    : Same as those used to run raxml. For example:
\&
\& $factory = Bio::Tools::Run::Phylo::Raxml\->new(\-p  => 100, \-SSE3 => 1)
.Ve
.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
\& Returns:  string
\& Args    :
.Ve
.SS "error_string"
.IX Subsection "error_string"
.Vb 5
\& Title   : error_string
\& Usage   : $obj\->error_string($newval)
\& Function: Where the output from the last analysus run is stored.
\& Returns : value of error_string
\& Args    : newvalue (optional)
.Ve
.SS "version"
.IX Subsection "version"
.Vb 6
\& Title   : version
\& Usage   : exit if $prog\->version() < 1.8
\& Function: Determine the version number of the program
\& Example :
\& Returns : float or undef
\& Args    : none
.Ve
.SS "quiet"
.IX Subsection "quiet"
.Vb 6
\& Title   : quiet
\& Usage   : 
\& Function: get or set value for \*(Aqquiet\*(Aq
\& Example :
\& Returns : 
\& Args    : the value
.Ve
.SS "run"
.IX Subsection "run"
.Vb 7
\& Title   : run
\& Usage   : $factory\->run($stockholm_file) OR
\&           $factory\->run($align_object)
\& Function: Runs Raxml 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 "_run"
.IX Subsection "_run"
.Vb 5
\& Title   : _run
\& Usage   : Internal function, not to be called directly
\& Function: Runs the application
\& Returns : Tree object
\& Args    : Alignment file name
.Ve
.SS "_write_alignfile"
.IX Subsection "_write_alignfile"
.Vb 5
\& Title   : _write_alignfile
\& Usage   : Internal function, not to be called directly
\& Function: Create an alignment file
\& Returns : filename
\& Args    : Bio::Align::AlignI
.Ve
.SS "_alphabet"
.IX Subsection "_alphabet"
.Vb 5
\& Title   : _alphabet
\& Usage   : my $alphabet = $self\->_alphabet;
\& Function: Get the alphabet of the input alignment, defaults to \*(Aqdna\*(Aq
\& Returns : \*(Aqdna\*(Aq or \*(Aqprotein\*(Aq
\& Args    : Alignment file
.Ve
.SS "_setparams"
.IX Subsection "_setparams"
.Vb 6
\& Title   :  _setparams
\& Usage   :  Internal function, not to be called directly    
\& Function:  Create parameter inputs for Raxml program
\& Example :
\& Returns : parameter string to be passed to Raxml
\& Args    : name of calling object
.Ve
.SH "Bio::Tools::Run::BaseWrapper methods"
.IX Header "Bio::Tools::Run::BaseWrapper methods"
.SS "no_param_checks"
.IX Subsection "no_param_checks"
Title   : no_param_checks
Usage   : \f(CW$obj\fR\->no_param_checks($newval)
Function: Boolean flag as to whether or not we should
          trust the sanity checks for parameter values  
Returns : value of no_param_checks
Args    : newvalue (optional)
.SS "save_tempfiles"
.IX Subsection "save_tempfiles"
Title   : save_tempfiles
Usage   : \f(CW$obj\fR\->save_tempfiles($newval)
Function: 
Returns : value of save_tempfiles
Args    : newvalue (optional)
.SS "outfile_name"
.IX Subsection "outfile_name"
Title   : outfile_name
Usage   : my \f(CW$outfile\fR = \f(CW$Raxml\fR\->\fBoutfile_name()\fR;
Function: Get/Set the name of the output file for this run
           (if you wanted to do something special)
Returns : string
Args    : [optional] string to set value to
.SS "tempdir"
.IX Subsection "tempdir"
Title   : tempdir
Usage   : my \f(CW$tmpdir\fR = \f(CW$self\fR\->\fBtempdir()\fR;
Function: Retrieve a temporary directory name (which is created)
Returns : string which is the name of the temporary directory
Args    : none
.SS "cleanup"
.IX Subsection "cleanup"
Title   : cleanup
Usage   : \f(CW$Raxml\fR\->\fBcleanup()\fR;
Function: Will cleanup the tempdir directory
Returns : none
Args    : none
.SS "io"
.IX Subsection "io"
Title   : io
Usage   : \f(CW$obj\fR\->io($newval)
Function:  Gets a Bio::Root::IO object
Returns : Bio::Root::IO
Args    : none