<commit_before>#
# You may distribute this module under the same terms as perl itself
#
# POD documentation - main docs before the code

=pod 

=head1 NAME

Bio::EnsEMBL::Compara::RunnableDB::PHYML

=cut

=head1 SYNOPSIS

my $db      = Bio::EnsEMBL::Compara::DBAdaptor->new($locator);
my $repmask = Bio::EnsEMBL::Compara::RunnableDB::PHYML->new ( 
                                                    -db      => $db,
                                                    -input_id   => $input_id
                                                    -analysis   => $analysis );
$repmask->fetch_input(); #reads from DB
$repmask->run();
$repmask->output();
$repmask->write_output(); #writes to DB

=cut

=head1 DESCRIPTION

This Analysis/RunnableDB is designed to take ProteinTree as input
This must already have a multiple alignment run on it.  It uses that alignment
as input into the PHYML program which then generates a phylogenetic tree

input_id/parameters format eg: "{'protein_tree_id'=>1234}"
    protein_tree_id : use 'id' to fetch a cluster from the ProteinTree

=cut

=head1 CONTACT

Describe contact details here
<commit_msg>added contact info to perldoc<commit_after>#
# You may distribute this module under the same terms as perl itself
#
# POD documentation - main docs before the code

=pod 

=head1 NAME

Bio::EnsEMBL::Compara::RunnableDB::PHYML

=cut

=head1 SYNOPSIS

my $db      = Bio::EnsEMBL::Compara::DBAdaptor->new($locator);
my $repmask = Bio::EnsEMBL::Compara::RunnableDB::PHYML->new ( 
                                                    -db      => $db,
                                                    -input_id   => $input_id
                                                    -analysis   => $analysis );
$repmask->fetch_input(); #reads from DB
$repmask->run();
$repmask->output();
$repmask->write_output(); #writes to DB

=cut

=head1 DESCRIPTION

This Analysis/RunnableDB is designed to take ProteinTree as input
This must already have a multiple alignment run on it.  It uses that alignment
as input into the PHYML program which then generates a phylogenetic tree

input_id/parameters format eg: "{'protein_tree_id'=>1234}"
    protein_tree_id : use 'id' to fetch a cluster from the ProteinTree

=cut

=head1 CONTACT

  Contact <NAME> on module implemetation/design detail: <EMAIL>
  Contact <NAME> on EnsEMBL/Compara: <EMAIL>
  Contact <NAME> on EnsEMBL in general: <EMAIL>

{'fraction_non_alphanumeric': 0.09597008724553385, 'fraction_numerical': 0.006647278770253427, 'mean_word_length': 2.572700296735905, 'pattern_counts': {'":': 0, '<': 9, '<?xml version=': 0, '>': 29, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 12, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '1362371', 'n_tokens_mistral': 751, 'n_tokens_neox': 700, 'n_words': 235}