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

✨ NAME ✨

Bio::TreeIO::lintree — a parser for lintree output trees 🌳

(yes bestie, this page is Bio::T...intree(3pm) from the User Contributed Perl Documentation, and it's giving very niche-but-iconic 💅)

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🦋 SYNOPSIS 🦋

# do not use directly, use through Bio::TreeIO
use Bio::TreeIO;
my $treeio = Bio::TreeIO->new(-format => 'lintree',
                             -file   => 't/data/crab.nj');
my $tree = $treeio->next_tree;

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🌸 DESCRIPTION 🌸

Okay so this is the parser for lintree output, and that output looks exactly like this, no cap:

  13 sequences     1000 bootstraping
1 A-salina
2 C-vittat
3 C-sp.
4 L-aequit
5 P-camtsc
6 E-tenuim
7 L-splend
8 P-bernha
9 P-acadia
10 P-p(NE)
11 P-p(GU)
12 P-l(NE)
13 P-l(GU)
 14 and   2        0.098857      1000
 14 and   3        0.127932      1000
 15 and   1        0.197471      1000
 15 and  14        0.029273       874
 16 and  10        0.011732      1000
 16 and  11        0.004529      1000
 17 and  12        0.002258      1000
 17 and  13        0.000428      1000
 18 and  16        0.017512      1000
 18 and  17        0.010824       998
 19 and   4        0.006534      1000
 19 and   5        0.006992      1000
 20 and  15        0.070461      1000
 20 and  18        0.030579       998
 21 and   8        0.003339      1000
 21 and   9        0.002042      1000
 22 and   6        0.011142      1000
 22 and  21        0.010693       983
 23 and  20        0.020714       996
 23 and  19        0.020350      1000
 24 and  23        0.008665       826
 24 and  22        0.013457       972
 24 and   7        0.025598      1000

Wanna know where the program itself lives? Hit up http://www.bio.psu.edu/People/Faculty/Nei/Lab/software.htm — that's the access point. And if you wanna cite the lore properly: N Takezaki, A Rzhetsky, and M Nei, "Phylogenetic test of the molecular clock and linearized trees." Mol Biol Evol 12(5):823-33. 📚

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💬 FEEDBACK 💬

🎀 Mailing Lists 🎀

User feedback is literally an integral part of the evolution of this and other Bioperl modules 🫶 so send your comments and suggestions preferably to the Bioperl mailing list. Your participation is so much appreciated, fr fr.

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, bestie 🙈 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 more detail the better, periodt.

🐛 Reporting Bugs 🐛

Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution — iconic teamwork behavior 👑 Bug reports can be submitted via the web:

https://github.com/bioperl/bioperl-live/issues

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💖 AUTHOR - Jason Stajich 💖

Email jason-at-bioperl-dot-org 📧

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🌈 CONTRIBUTORS 🌈

Ideas and discussion from:

• Alan Christoffels
• Avril Coghlan

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📖 APPENDIX 📖

The rest of the documentation details each of the object methods, so grab a snack 🍓 Internal methods are usually preceded with a _

💅 new 💅

• Title : new
• Usage : my $obj = Bio::TreeIO::lintree->new();
• Function: Builds a new Bio::TreeIO::lintree object
• Returns : an instance of Bio::TreeIO::lintree
• Args : -nodetype => Node type to create [default Bio::Tree::Node]

✨ next_tree ✨

• Title : next_tree
• Usage : my $tree = $treeio->next_tree
• Function: Gets the next tree in the stream
• Returns : Bio::Tree::TreeI
• Args : none

🧚 nodetype 🧚

• Title : nodetype
• Usage : $obj->nodetype($newval)
• Function: (blank in the source, bestie — nothing there)
• Example : (also blank, that's just how it is)
• Returns : value of nodetype (a scalar)
• Args : on set, new value (a scalar or undef, optional)

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And that's the whole vibe check, bestie — go parse some trees 🌳💜

Signing off from perl v5.32.1, dated 2021-08-15, on page Bio::T...intree(3pm) — slay, mwah 💅✨