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

💖 Bio::T...ickTree(3pm) 💖

okay so bestie, welcome to the User Contributed Perl Documentation for Bio::T...ickTree(3pm) — yes that's the short lil nickname, the whole thing is Bio::Tools::Run::Phylo::QuickTree and it's giving phylogeny speedrun energy. grab a strawberry 🍓 and let's get into it.

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✨ NAME ✨

Bio::Tools::Run::Phylo::QuickTree — it's a wrapper for rapid reconstruction of phylogenies using QuickTree. literally that's the whole job. no cap. 🌳

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🌸 SYNOPSIS 🌸

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 = 't/data/cysprot.stockholm';
$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);

so you make a factory, you hand it an alignment, you get a tree back. iconic behavior honestly. 💅

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🦋 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/

Currently only input with alignments and output of trees is supported. (Ie. no support for distance matrix in/out.) so like, don't come for her with a distance matrix, she will not know her. 🙈

You will need to enable this QuickTree wrapper to find the quicktree program. This can be done in (at least) three ways:

1. Make sure the QuickTree executable is in your path. ✅
2. Define an environmental variable QUICKTREEDIR which is a directory which contains the 'quicktree' 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} = '/home/username/quicktree_1.1/bin' }
use Bio::Tools::Run::Phylo::QuickTree;

pick your fighter, any of the three works. slay ✨

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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 the Bioperl mailing list. Your participation is much appreciated. fr fr, they wanna hear from you. 😭💖

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. (the typo "reponsive" is canon, we don't fix canon) 🧚

🐛 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:

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

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👑 AUTHOR - Sendu Bala 👑

Email bix@sendu.me.uk — main character energy, thank you Sendu 💜

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📖 APPENDIX 📖

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

⭐ 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, obtained from ENV variable.
• Returns : string
• Args : None

⭐ new ⭐

• 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]

⭐ upgma ⭐

• 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.

⭐ kimura ⭐

• 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.

⭐ boot ⭐

• 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.

⭐ run ⭐

• 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).

⭐ _setparams ⭐

• 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

bestie this one is internal, do not call it directly, okay? hands off. 🙅♀️

⭐ _writeAlignFile ⭐

• Title : _writeAlignFile
• Usage : obj->_writeAlignFile($seq)
• Function: Internal (not to be used directly)
• Returns : filename
• Args : Bio::Align::AlignI

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and that's the whole page, you ate that 🎀

little sign-off bestie: this doc came from perl v5.36.0, dated 2023-01-22, and it lives under the Bio::T...ickTree(3pm) manual name. bye pookie, go build a tree 🌈🌳💖