Bio::T...::Raxml(3pm)

📦
version 1.7.3 · 3 versions
, in debian bookworm, ubuntu noble

✨ NAME ✨

Bio::Tools::Run::Phylo::Raxml — Bio::Tree getter from DNA alignment through raxml. that's the whole assignment bestie, it takes your alignment and hands you back a tree 🌳 no cap.

🎀 SYNOPSIS 🎀

okay so here's the group-chat version of how you actually use this 💖

  # Build a Raxml factory
  $factory = Bio::Tools::Run::Phylo::Raxml->new(-p  => 100);

  # Get an alignment
  my $alignio = Bio::AlignIO->new(
        -format => 'fasta',
        -file   => '219877.cdna.fasta');
  my $alnobj = $alignio->next_aln;

  # Analyze the aligment and get a Tree
  my $tree = $factory->run($alnobj);

build the factory → grab your alignment → run it → boom, tree. three steps, that's the entire main character arc ✨

🌸 DESCRIPTION 🌸

Get a Bio::Tree object using raxml given a protein or DNA alignment. that's literally it. protein or DNA, it does not care, it will eat either one 🧬💅

💌 FEEDBACK 💌

📬 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://bioperl.org/wiki/Mailing_lists  - About the mailing lists

🩹 Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

Do not contact the module maintainer directly. fr fr, don't do it.

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 — the more detail you give, the faster someone can help you out 🙈

🐛 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://redmine.open-bio.org/projects/bioperl/

👑 AUTHOR - Brian Osborne 👑

Email briano@bioteam.net

📖 APPENDIX 📖

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _. (iykyk — if it starts with an underscore, it's not for you, stay out of the kitchen 💀)

🌟 new

  • 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)

🌟 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
  • Returns: string
  • Args: (nothing listed, it just vibes)

🌟 error_string

  • 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)

🌟 version

  • Title: version
  • Usage: exit if $prog->version() < 1.8
  • Function: Determine the version number of the program
  • Example: (nope, nothing here)
  • Returns: float or undef
  • Args: none

🌟 quiet

  • Title: quiet
  • Usage: (empty, respectfully)
  • Function: get or set value for 'quiet'
  • Example: (empty)
  • Returns: (empty)
  • Args: the value

🌟 run

  • 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).

🌟 _run

  • Title: _run
  • Usage: Internal function, not to be called directly
  • Function: Runs the application
  • Returns: Tree object
  • Args: Alignment file name

🌟 _write_alignfile

  • Title: _write_alignfile
  • Usage: Internal function, not to be called directly
  • Function: Create an alignment file
  • Returns: filename
  • Args: Bio::Align::AlignI

🌟 _alphabet

  • Title: _alphabet
  • Usage: my $alphabet = $self->_alphabet;
  • Function: Get the alphabet of the input alignment, defaults to 'dna'
  • Returns: 'dna' or 'protein'
  • Args: Alignment file

🌟 _setparams

  • Title: _setparams
  • Usage: Internal function, not to be called directly
  • Function: Create parameter inputs for Raxml program
  • Example: (empty)
  • Returns: parameter string to be passed to Raxml
  • Args: name of calling object

🧚 Bio::Tools::Run::BaseWrapper methods 🧚

the inherited bestie methods, handed down like a family recipe 🍓

no_param_checks

  • Title: no_param_checks
  • Usage: $obj->no_param_checks($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)

save_tempfiles

  • Title: save_tempfiles
  • Usage: $obj->save_tempfiles($newval)
  • Function: (nothing listed — mysterious, iconic)
  • Returns: value of save_tempfiles
  • Args: newvalue (optional)

outfile_name

  • Title: outfile_name
  • Usage: my $outfile = $Raxml->outfile_name();
  • 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

tempdir

  • Title: tempdir
  • Usage: my $tmpdir = $self->tempdir();
  • Function: Retrieve a temporary directory name (which is created)
  • Returns: string which is the name of the temporary directory
  • Args: none

cleanup

  • Title: cleanup
  • Usage: $Raxml->cleanup();
  • Function: Will cleanup the tempdir directory
  • Returns: none
  • Args: none

io

  • Title: io
  • Usage: $obj->io($newval)
  • Function: Gets a Bio::Root::IO object
  • Returns: Bio::Root::IO
  • Args: none

and that's the whole page bestie, you ate 💅

this manual is Bio::T...::Raxml(3pm), generated from perl v5.36.0 and dated 2023-01-22. go build a tree, you've got this 🌈🦋💖

📦 where this page comes from