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

💖 Bio::Tools::Run::Phylo::Phylip::Neighbor 💖

hii bestie 🫶 welcome to the User Contributed Perl Documentation page for Bio::Tools::Run::Phylo::Phylip::Neighbor, and no cap it's a whole vibe. Also, tiny historical tea: this landed 14 Nov 2002, credit to Shawn, and it Works with Phylip version 3.6.

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🌸 NAME 🌸

Bio::Tools::Run::Phylo::Phylip::Neighbor — it's a wrapper for the phylip program neighbor by Joseph Felsenstein, and its whole job is creating a phylogenetic tree (either through Neighbor or UPGMA) based on protein distances based on amino substitution rate. that's it, that's the gig 💅

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✨ SYNOPSIS ✨

okay so here's the full glow-up, step by step, exactly as written:

  #Create a SimpleAlign object
  @params = ('ktuple' => 2, 'matrix' => 'BLOSUM');
  $factory = Bio::Tools::Run::Alignment::Clustalw->new(@params);
  $inputfilename = 't/data/cysprot.fa';
  $aln = $factory->run($inputfilename); # $aln is a SimpleAlign object.

  # Create the Distance Matrix
  # using a default PAM matrix and id name lengths limit of 30 note to
  # use id name length greater than the standard 10 in neighbor, you
  # will need to modify the neighbor source code

  $protdist_factory = Bio::Tools::Run::Phylo::Phylip::ProtDist->new(@params);
  my $matrix  = $protdist_factory->run($aln);

  #Create the tree passing in the distance matrix
  @params = ('type'=>'NJ','outgroup'=>2,'lowtri'=>1,
             'upptri'=>1,'subrep'=>1);

  my $neighbor_factory =
     Bio::Tools::Run::Phylo::Phylip::Neighbor->new(@params);

  #you can set your outgroup using either a number specifying
  #the rank in the matrix or you can just use the name of the
  #species

  $neighbor_factory->outgroup('ENSP00001');
  #or
  $neighbor_factory->outgroup(1);

  my ($tree) = $neighbor_factory->run($matrix);

  # Alternatively, one can create the tree by passing in a file name
  # containing a phylip formatted distance matrix(using protdist)
  my $neighbor_factory =
    Bio::Tools::Run::Phylo::Phylip::Neighbor->new(@params);
  my ($tree) = $neighbor_factory->run('/home/shawnh/prot.dist');

  # To prevent PHYLIP from truncating sequence names:
  # Step 1. Shelf the original names:
    my ($aln_safe, $ref_name)=                    #   $aln_safe has serial names
               $aln->set_displayname_safe();      #   $ref_name holds original names
  # Step 2. Run ProtDist and Neighbor:
    $matrix  = $protdist_factory->
                creat_distance_matrix($aln_safe); #  Use $aln_safe instead of $aln
    $tree = $neighbor_factory->run($matrix);
  # Step 3. Retrieve orgininal OTU names:
    use Bio::Tree::Tree;
    my @nodes=$tree->get_nodes();
    foreach my $nd (@nodes){
       $nd->id($ref_name->{$nd->id_output}) if $nd->is_Leaf;
    }

heads up bestie 🚨 see that note about the id name lengths? if you want id names longer than the standard 10 in neighbor, you literally have to go modify the neighbor source code yourself. the wrapper can't do it for you, no matter how cute you ask.

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🎀 PARAMTERS FOR NEIGHBOR COMPUTATION 🎀

(yes the heading says PARAMTERS, we don't fix it, we respect it 💀)

👑 TYPE

• Title: TYPE
• Description: (optional) This sets the type of tree to construct, using neighbor joining or UPGMA.
  • NJ — Neighbor Joining
  • UPGMA — UPGMA
• Usage: @params = ('type'=>'X');#where X is one of the values above Defaults to NJ. For more information on the usage of the different models, please refer to the documentation found in the phylip package.

🦋 OUTGROUP (*ONLY AVAILABLE FOR NEIGHBOR JOINING)

• Title: OUTGROUP
• Description: (optional) This option selects the species to be used as the outgroup.
• Acceptable Values: integer
• Usage: @params = ('outgroup'=>'X'); where X is an positive integer not more than the number of sequences. Defaults to 1.

💜 LOWTRI

• Title: LOWTRI
• Description: (optional) This indicates that the distance matrix is input in Lower-triangular form (the lower-left half of the distance matrix only, without the zero diagonal elements).
• Usage: @params = ('lowtri'=>'X'); where X is either 1 or 0 Defaults to 0.

🌈 UPPTRI

• Title: UPPTRI
• Description: (optional) This indicates that the distance matrix is input in upper-triangular form (the upper-right half of the distance matrix only, without the zero diagonal elements.)
• Usage: @params = ('upptri'=>'X'); where X is either 1 or 0 Defaults to 0.

🍓 SUBREP

• Title: SUBREP
• Description: (optional) This is the Subreplication option. It informs the program that after each distance will be provided an integer indicating that the distance is a mean of that many replicates.
• Usage: @params = ('subrep'=>'X'); where X is either 1 or 0 Defaults to 0.

✨ JUMBLE

• Title: JUMBLE
• Description: (optional) This enables you to tell the program to use a random number generator to choose the input order of species. seed: an integer between 1 and 32767 and of the form 4n+1 which means that it must give a remainder of 1 when divided by 4. Each different seed leads to a different sequence of addition of species. By simply changing the random number seed and re-running programs one can look for other, and better trees. iterations:
• Usage: @params = ('jumble'=>'17); where 17 is the random seed Defaults to no jumble.

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💬 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

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 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/

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👑 AUTHOR - Shawn Hoon 👑

Email shawnh@fugu-sg.org

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🌟 CONTRIBUTORS 🌟

Email:jason-at-bioperl.org

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📖 APPENDIX 📖

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _.

🧚 program_name

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

🧚 program_dir

• Title: program_dir
• Usage: ->program_dir()
• Function: returns the program directory, obtained from ENV variable.
• Returns: string
• Args:

🧚 idlength

• Title: idlength
• Usage: $obj->idlength ($newval)
• Function:
• Returns: value of idlength
• Args: newvalue (optional)

(no, the Function line is genuinely empty in the source, we're not hiding anything from you 💜)

🧚 run

• Title: run
• Usage:

$inputfilename = 't/data/prot.dist';
$tree = $neighborfactory->run($inputfilename);

or

$protdist_factory = Bio::Tools::Run::Phylo::Phylip::ProtDist->new(@params);
$matrix  = $protdist_factory->create_distance_matrix($aln);
$tree= $neighborfactory->run($matrix);

• Function: a Bio:Tree from a protein distance matrix created by protidst
• Example:
• Returns: Bio::Tree
• Args: Name of a file containing a protein distance matrix in Phylip format or a hash ref to a matrix

drama warning 😭 Throws an exception if argument is not either a string (eg a filename) or a Hash. If argument is string, throws exception if file corresponding to string name can not be found.

🧚 create_tree

• Title: create_tree
• Usage: my $file = $app->create_tree($treefile);
• Function: This method is deprecated. Please use run method.
• Returns: File containing the rendered tree
• Args: either a Bio::Tree::TreeI OR filename of a tree in newick format

🧚 _run

• Title: _run
• Usage: Internal function, not to be called directly
• Function: makes actual system call to neighbor program
• Example:
• Returns: Bio::Tree object
• Args: Name of a file containing protein distances in Phylip format and a parameter string to be passed to neighbor

🧚 _setinput()

• Title: _setinput
• Usage: Internal function, not to be called directly
• Function: Create input file for neighbor program
• Example:
• Returns: name of file containing the protein distance matrix in Phylip format
• Args: name of file created by protdist or ref to hash created by Bio::Tools:Run::Phylo::Phylip::ProtDist

🧚 names()

• Title: names
• Usage: $tree->names(\%names)
• Function: get/set for a hash ref for storing names in matrix with rank as values.
• Example:
• Returns: hash reference
• Args: hash reference

🧚 _setparams()

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

🧚 outfile

• Title: outfile
• Usage: $obj->outfile($newval)
• Function: Get/Set default PHYLIP outfile name (outfile usually)
• Returns: value of outfile
• Args: newvalue (optional)

🧚 treefile

• Title: treefile
• Usage: $obj->treefile($newval)
• Function: Get/Set the default PHYLIP treefile name (treefile usually)
• Returns: value of treefile
• Args: newvalue (optional)

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that's the whole page bestie, you ate it 🍽️✨ go build some trees and stay iconic. this documentation was served up by perl v5.36.0, dated 2023-01-22, and it's Bio::T...ighbor(3pm) — mwah 💋🌸💅