Bio::T...lo::LVB(3pm)

💖 Bio::Tools::Run::Phylo::LVB 💖

okay so bestie, this is a page from the User Contributed Perl Documentation for the module Bio::Tools::Run::Phylo::LVB (a 3pm manpage, iykyk). It's an object for driving the LVB program so you can get an array of Bio::Tree objects out of a nucleotide multiple alignment file, or out of a nucleotide SimpleAlign object. It plays nice with LVB version 2.1 and nothing else, so don't come for it. ✨

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🌸 NAME 🌸

Bio::Tools::Run::Phylo::LVB — it's the object that runs LVB for you, and hands back an array of Bio::Tree objects made from either a nucleotide multiple alignment file or a nucleotide SimpleAlign object. Works with LVB version 2.1. 💅

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🦋 SYNOPSIS 🦋

use Bio::Tools::Run::Phylo::LVB;

# Create a SimpleAlign object.
# NOTE. Aligning nucleotide sequence directly, as below, makes
# sense for non-coding nucleotide sequence (e.g., structural RNA
# genes, introns, ITS). For protein-coding genes, to prevent
# Clustal intronducing frameshifts one should instead align the
# translations of the genes, then convert the multiple alignment
# to nucleotide by referring to the corresponding transcript
# sequences (e.g., using EMBOSS tranalign).
use Bio::Tools::Run::Alignment::Clustalw;
$aln_factory = Bio::Tools::Run::Alignment::Clustalw->new(quiet => 1);
$inputfilename = "/Users/daniel/nuc.fa";
$aln = $aln_factory->align($inputfilename);

# Create the tree or trees.
$tree_factory = Bio::Tools::Run::Phylo::LVB->new(quiet => 1);
@trees = $tree_factory->run($aln);

# Or one can pass in a file name containing a nucleotide multiple
# alignment in Phylip 3.6 format:
$tree_factory = Bio::Tools::Run::Phylo::LVB->new(quiet => 1);
$tree = $tree_factory->run("/Users/daniel/nuc.phy");

quick heads up bestie 🚨 — that note up there in the code is important: aligning raw nucleotide sequence like that is the move for non-coding nucleotide sequence (think structural RNA genes, introns, ITS). But for protein-coding genes, if you don't wanna let Clustal introduce frameshifts, you align the translations of the genes instead, then convert the multiple alignment back to nucleotide by referring to the corresponding transcript sequences (like with EMBOSS tranalign). no cap. 🫶

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🎀 DESCRIPTION 🎀

It's a wrapper for LVB. LVB uses a simulated annealing heuristic search to go hunting for parsimonious trees starting from a nucleotide multiple alignment. it's giving "let the algorithm cook". 🔥

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💌 FEEDBACK 💌

Mailing Lists

User feedback is literally an integral part of the evolution of this and other Bioperl modules — like, the whole thing thrives on it. Send your comments and suggestions preferably to one of the Bioperl mailing lists, and 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, ok bestie? There are lots of experienced and reponsive experts who'll look at the problem and quickly address it. And please include a thorough description of the problem with code and data examples if at all possible — help them help you. 🙏

Reporting Bugs

Report bugs to the Bioperl bug tracking system so we can keep track of the bugs and their resolution. Bug reports can be submitted via the web:

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

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✨ PARAMETERS FOR LVB COMPUTATION ✨

FORMAT

• Title : FORMAT
• Description : (optional) When you're running LVB from a Phylip 3.6-format multiple alignment file, this says what the layout of the file is. It may be "interleaved" or "sequential". FORMAT gets automatically set to "interleaved" if you're running from a SimpleAlign object. Defaults to "interleaved".

GAPS

• Title : GAPS
• Description : (optional) LVB can treat gaps represented in the multiple alignment by "-" as either "fifthstate" or "unknown". "fifthstate" treats "-" as equivalent to "O", which is an unambiguous character state that's distinct from all nucleotides. "unknown" treats "-" as equivalent to "?", which is an ambiguous site that may contain "A" or "C" or "G" or "T" or "O". Defaults to "unknown".

SEED

• Title : SEED
• Description : (optional) This specifies the random number seed for LVB. SEED has to be an integer in the range 0 to 900000000 inclusive. If you don't specify a seed, LVB takes one from the system clock. By default, no seed is specified.

DURATION

• Title : DURATION
• Description : (optional) This specifies the duration of the analysis, and it may be "fast" or "slow". "slow" makes LVB do a more thorough and more time-consuming search than "fast" does. Defaults to "slow".

BOOTSTRAPS

• Title : BOOTSTRAPS
• Description : (optional) This specifies how many bootstrap replicates to use, and it has to be a positive integer. Set bootstraps to 0 for no bootstrapping. Defaults to 0.

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👑 AUTHOR 👑

Daniel Barker

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🌈 CONTRIBUTORS 🌈

Email jason-AT-bioperl_DOT_org

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💜 APPENDIX 💜

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ (you know the vibe — underscore means "not for you, bestie, this is backstage"). 🙈

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 undef
• Args :

run

• Title : run
• Usage :

$inputfilename = '/Users/daniel/nuc.phy';
@trees = $factory->run($inputfilename);

• Function : Create one or more LVB trees from a SimpleAlign object or a file containing a Phylip 3.6-format nucleotide multiple alignment.
• Example :
• Returns : Array of L<Bio::Tree> objects
• Args : Name of a file containing a nucleotide multiple alignment in Phylip 3.6 format, or a SimpleAlign object

create_tree

• Title : create_tree
• Usage :

$inputfilename = '/Users/daniel/nuc.phy';
@trees = $factory->create_tree($inputfilename);

• Function : Create one or more LVB trees from a SimpleAlign object or a file containing a Phylip 3.6-format nucleotide multiple alignment.
• Example :
• Returns : Array of L<Bio::Tree> objects
• Args : Name of a file containing a nucleotide multiple alignment in Phylip 3.6 format, or a SimpleAlign object

_run

• Title : _run
• Usage : Internal function, not to be called directly
• Function : makes actual system call to lvb program
• Example :
• Returns : Array of Bio::Tree objects
• Args : Name of a file containing a multiple alignment in Phylip 3.6 format and a parameter string to be passed to LVB

_setinput

• Title : _setinput
• Usage : Internal function, not to be called directly
• Function : Create input file for lvb program
• Example :
• Returns : name of file containing a multiple alignment in Phylip 3.6 format
• Args : SimpleAlign object reference or input file name

_setparams

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

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okay and that's the whole thing, bestie, you made it to the end 🎉 this iconic little doc shipped as part of perl v5.36.0, dated 2023-01-22, and it lives under the manual page name Bio::T...lo::LVB(3pm) — periodt. go build some trees 💖🌳✨