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

📦

version 1.7.3 · 3 versions

1.7.3 · debian bookworm, debian trixie (latest)
1.7.3 · ubuntu jammy
1.7.3 · ubuntu noble

💖 NAME 💖

Bio::Tools::Phylo::PAML::ModelResult — okay so bestie, this is the container for an NSSite Model Result from PAML. it holds one model's whole little situation. it's giving "glorified box, but a VERY important box" ✨

🎀 VERSION 🎀

version 1.7.3 — that's the one, no cap. 💅

🦋 SYNOPSIS 🦋

here's the whole flow, start to finish. you grab a PAML::Result object, then you loop through every model it's holding and pull the deets out of each one:

# get a ModelResult from a PAML::Result object
use Bio::Tools::Phylo::PAML;
my $paml = Bio::Tools::Phylo::PAML->new(-file => 'mlc');
my $result = $paml->next_result;
foreach my $model ( $result->get_NSSite_results ) {
  print $model->model_num, " ", $model->model_description, "\n";
  print $model->kappa, "\n";
  print $model->run_time, "\n";
# if you are using PAML < 3.15 then only one place for POS sites
 for my $sites ( $model->get_pos_selected_sites ) {
  print join("\t",@$sites),"\n";
 }
# otherwise query NEB and BEB slots
 for my $sites ( $model->get_NEB_pos_selected_sites ) {
   print join("\t",@$sites),"\n";
 }

 for my $sites ( $model->get_BEB_pos_selected_sites ) {
  print join("\t",@$sites),"\n";
 }

}

lowkey the important plot twist here: if you're on PAML < 3.15 there's only one place for POS sites (get_pos_selected_sites). otherwise you go query the NEB and BEB slots instead. iykyk 🧚

🛠️ METHODS 🛠️

`new` 🌸

birthing a brand-new object, the classic.

Title: new
Usage: my $obj = Bio::Tools::Phylo::PAML::ModelResult->new();
Function: Builds a new Bio::Tools::Phylo::PAML::ModelResult object 🫶
Returns: an instance of Bio::Tools::Phylo::PAML::ModelResult
Args:
- -model_num — model number
- -model_description — model description
- -kappa — value of kappa
- -time_used — amount of time
- -pos_sites — arrayref of sites under positive selection
- -neb_sites — arrayref of sites under positive selection (by NEB analysis)
- -beb_sites — arrayref of sites under positive selection (by BEB analysis)
- -trees — arrayref of tree(s) data for this model
- -shape_params — hashref of parameters, and it's legit one of these two shapes:

( 'shape' => 'alpha',
  'gamma' => $g,
  'r' => $r,
  'f' => $f
)

( 'shape' => 'beta',
  'p' => $p,
  'q' => $q
)

-likelihood — likelihood
-num_site_classes — number of site classes
-dnds_site_classes — hashref with two keys, 'p' and 'w', which each point to an array; each slot is for a different site class. 'w' is for dN/dS and 'p' is probability

`model_num` ⭐

Title: model_num
Usage: $obj->model_num($newval)
Function: Get/Set the Model number (0,1,2,3...)
Returns: value of model_num (a scalar)
Args: on set, new value (a scalar or undef, optional)

`model_description` 💜

Title: model_description
Usage: $obj->model_description($newval)
Function: Get/Set the model description. this is something like 'one-ratio', 'neutral', 'selection' ✨
Returns: value of description (a scalar)
Args: on set, new value (a scalar or undef, optional)

`time_used` ⏰

Title: time_used
Usage: $obj->time_used($newval)
Function: Get/Set the time it took to run this analysis
Returns: value of time_used (a scalar)
Args: on set, new value (a scalar or undef, optional)

`kappa` 💫

Title: kappa
Usage: $obj->kappa($newval)
Function: Get/Set kappa (ts/tv)
Returns: value of kappa (a scalar)
Args: on set, new value (a scalar or undef, optional)

`num_site_classes` 🔢

Title: num_site_classes
Usage: $obj->num_site_classes($newval)
Function: Get/Set the number of site classes for this model
Returns: value of num_site_classes (a scalar)
Args: on set, new value (a scalar or undef, optional)

`dnds_site_classes` 🌈

Title: dnds_site_classes
Usage: $obj->dnds_site_classes($newval)
Function: Get/Set dN/dS site classes, a hashref with 2 keys, 'p' and 'w', which point to arrays — one slot for each site class.
Returns: value of dnds_site_classes (a hashref)
Args: on set, new value (a scalar or undef, optional)

`get_pos_selected_sites` 👑

Title: get_pos_selected_sites
Usage: my @sites = $modelresult->get_pos_selected_sites();
Function: Get the sites which PAML has identified as under positive selection (w > 1). this returns an array with each slot being a site, 4 values:
- site location (in the original alignment)
- Amino acid (I think in the first sequence)
- P (P value)
- Significance (** indicated > 99%, * indicates >=95%)
Returns: Array
Args: none

`add_pos_selected_site` 🍓

Title: add_pos_selected_site
Usage: $result->add_pos_selected_site($site,$aa,$pvalue,$signif);
Function: Add a site to the list of positively selected sites
Returns: count of the number of sites stored
Args:
- $site — site number (in the alignment)
- $aa — amino acid under selection
- $pvalue — float from 0->1 represent probability site is under selection according to this model
- $signif — significance (coded as either empty, '*', or '**'

`get_NEB_pos_selected_sites` 🧚

Title: get_NEB_pos_selected_sites
Usage: my @sites = $modelresult->get_NEB_pos_selected_sites();
Function: Get the sites which PAML has identified as under positive selection (w > 1) using Naive Empirical Bayes. this returns an array with each slot being a site, 4 values:
- site location (in the original alignment)
- Amino acid (I think in the first sequence)
- P (P value)
- Significance (** indicated > 99%, * indicates > 95%)
- post mean for w
Returns: Array
Args: none

`add_NEB_pos_selected_site` 🦋

Title: add_NEB_pos_selected_site
Usage: $result->add_NEB_pos_selected_site($site,$aa,$pvalue,$signif);
Function: Add a site to the list of positively selected sites
Returns: count of the number of sites stored
Args:
- $site — site number (in the alignment)
- $aa — amino acid under selection
- $pvalue — float from 0->1 represent probability site is under selection according to this model
- $signif — significance (coded as either empty, '*', or '**'
- $postmean — post mean for w

`get_BEB_pos_selected_sites` 🌟

Title: get_BEB_pos_selected_sites
Usage: my @sites = $modelresult->get_BEB_pos_selected_sites();
Function: Get the sites which PAML has identified as under positive selection (w > 1) using Bayes Empirical Bayes. this returns an array with each slot being a site, 6 values:
- site location (in the original alignment)
- Amino acid (I think in the first sequence)
- P (P value)
- Significance (** indicated > 99%, * indicates > 95%)
- post mean for w (mean)
- Standard Error for w (SE)
Returns: Array
Args: none

`add_BEB_pos_selected_site` 🎀

Title: add_BEB_pos_selected_site
Usage: $result->add_BEB_pos_selected_site($site,$aa,$pvalue,$signif);
Function: Add a site to the list of positively selected sites
Returns: count of the number of sites stored
Args:
- $site — site number (in the alignment)
- $aa — amino acid under selection
- $pvalue — float from 0->1 represent probability site is under selection according to this model
- $signif — significance (coded as either empty, '*', or '**'
- $postmean — post mean for w
- $SE — Standard Error for w

`next_tree` 🌳

Title: next_tree
Usage: my $tree = $factory->next_tree;
Function: Get the next tree from the factory
Returns: L<Bio::Tree::TreeI>
Args: none

`get_trees` 🌲

Title: get_trees
Usage: my @trees = $result->get_trees;
Function: Get all the parsed trees as an array
Returns: Array of trees
Args: none

`rewind_tree_iterator` ⏪

Title: rewind_tree_iterator
Usage: $result->rewind_tree_iterator()
Function: Rewinds the tree iterator so that next_tree can be called again from the beginning
Returns: none
Args: none

`add_tree` 🌴

Title: add_tree
Usage: $result->add_tree($tree);
Function: Adds a tree
Returns: integer which is the number of trees stored
Args: L<Bio::Tree::TreeI>

`shape_params` 💠

Title: shape_params
Usage: $obj->shape_params($newval)
Function: Get/Set shape params for the distribution, 'alpha', 'beta' which is a hashref with 1 keys, 'p' and 'q'
Returns: value of shape_params (a scalar)
Args: on set, new value (a scalar or undef, optional)

`likelihood` 📈

Title: likelihood
Usage: $obj->likelihood($newval)
Function: log likelihood
Returns: value of likelihood (a scalar)
Args: on set, new value (a scalar or undef, optional)

💌 FEEDBACK 💌

Mailing lists 📬

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

bioperl-l@bioperl.org              - General discussion
http://bioperl.org/Support.html    - 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 responsive 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 of the bugs and their resolution. bug reports can be submitted via the web:

https://github.com/bioperl/bio-tools-phylo-paml/issues

✍️ AUTHOR ✍️

Jason Stajich <jason@bioperl.org> — the icon, the moment, the main character 💅

this software is copyright (c) by Jason Stajich <jason@bioperl.org>.

this software is available under the same terms as the perl 5 programming language system itself.

okay that's the whole page bestie, you ate 💖 this was Bio::T...Result(3pm) from the User Contributed Perl Documentation — perl v5.34.0, dated 2022-10-14. go forth and model your sites, queen 👑✨

📦 where this page comes from

debian bookworm: libbio-tools-phylo-paml-perl 1.7.3-4 · Artistic-1.0-Perl OR GPL-1.0-or-later
debian trixie: libbio-tools-phylo-paml-perl 1.7.3-4 · Artistic-1.0-Perl OR GPL-1.0-or-later
💖 girlified by deepseek-ai/DeepSeek-V4.1-Flash on 2026-11-03: a language model's rewrite of the original, under its terms

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

💖 NAME 💖

🎀 VERSION 🎀

🦋 SYNOPSIS 🦋

🛠️ METHODS 🛠️

new 🌸

model_num ⭐

model_description 💜

time_used ⏰

kappa 💫

num_site_classes 🔢

dnds_site_classes 🌈

get_pos_selected_sites 👑

add_pos_selected_site 🍓

get_NEB_pos_selected_sites 🧚

add_NEB_pos_selected_site 🦋

get_BEB_pos_selected_sites 🌟

add_BEB_pos_selected_site 🎀

next_tree 🌳

get_trees 🌲

rewind_tree_iterator ⏪

add_tree 🌴

shape_params 💠

likelihood 📈