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Bio::OntologyIO::simplehierarchy is a base class parser for simple hierarchy-by-indentation type formats. SYNOPSIS use Bio::OntologyIO; # do not use directly -- use via Bio::OntologyIO my $parser = Bio::OntologyIO->new ( -format => "simplehierarchy", -file => "pathology_terms.csv",...

W3C-PHP is a little php-cli script that can validate a list of URLs trough the W3C validator Web site (http://validator.w3.org/) with PHP-DOM functions. Configuration: list.txt -> contain the list of url that you need to validate the URLs must start with ":" without the "http://" prefix for...

PHP P10 Oper Services project is a small IRCD operator services written in the PHP scripting language. It supports levels, and it uses a database. It currently supports the IRCU P10+ IRC server and the PostgreSQL database. Whats New in This Release: - PHP Oper Services Alpha 1 PL1 This is a...


Platforms: *nix

Andys PHP Knowledgebase using MySQL is a database driven knowledgebase management system. Andys PHP Knowledgebase includes bookmark friendly URLs, Q&A, easy search with browsing by category, article submission, a powerful administrator interface and a professional and attractive interface..


Platforms: *nix

PHP music player controller (PMPC) is a script that allows navigation through your music directory, and the adding of albums or single songs into a playlist. The project also allows you to play, stop, pause, and go back and forth through the playlist. Apache needs to run as the same user that...


Platforms: *nix

Bio::Tools::Run::PiseWorkflow is a class to create a Pise workflow using Pise application objects as methods. A workflow is defined by a set of methods which all instanciate the class PiseApplication. SYNOPSIS # First, create a Bio::Tools::Run::AnalysisFactory::Pise object: my $factory = new...


Platforms: *nix

Bio::Tools::AlignFactory is a base object for alignment factories. SYNOPSIS You wont be using this as an object, but using a dervied class like Bio::Tools::pSW Holds common Alignment Factory attributes in place.


Platforms: *nix

Bio::Tools::Run::TribeMCL is a method for clustering proteins into related groups, which are termed protein families. SYNOPSIS use Bio::Tools::Run::TribeMCL; use Bio::SearchIO; # 3 methods to input the blast results # straight forward raw blast output (NCBI or WU-BLAST) my @params =...


Platforms: *nix

Bio::NEXUS::Block is a Perl module that provides useful functions for blocks in NEXUS file (parent class). SYNOPSIS This module is the super class of all NEXUS block classes. It is not used specifically from a program; in other words, you dont create a new Bio::NEXUS::Block object. Other...


Platforms: *nix

Bio::NEXUS::Node is a Perl module that provides functions for manipulating nodes in trees. SYNOPSIS new Bio::NEXUS::Node; METHODS new Title : new Usage : $node = new Bio::NEXUS::Node(); Function: Creates a new Bio::NEXUS::Node object Returns : Bio::NEXUS::Node object Args : none...


Platforms: *nix

Bio::NEXUS::TaxaBlock is a Perl module that represents TAXA block of a NEXUS file. SYNOPSIS if ( $type =~ /taxa/i ) { $block_object = new Bio::NEXUS::TaxaBlock($type, $block, $verbose); } If a NEXUS block is a taxa block, this module parses the block and stores the taxonomic data....


Platforms: *nix

Bio::NEXUS::TreesBlock is a Perl module that represents TREES block of a NEXUS file. SYNOPSIS if ( $type =~ /trees/i ) { $block_object = new Bio::NEXUS::TreesBlock( $block_type, $block, $verbose ); } If a NEXUS block is a Trees Block, this module parses the block and stores the tree data....


Platforms: *nix

Bio::Restriction::Enzyme is a single restriction endonuclease (cuts DNA at specific locations). SYNOPSIS # set up a single restriction enzyme. This contains lots of # information about the enzyme that is generally parsed from a # rebase file and can then be read back use...


Platforms: *nix

Bio::Root::Object is a core Perl 5 object. SYNOPSIS # Use this module as the root of your inheritance tree. Object Creation require Bio::Root::Object; $dad = new Bio::Root::Object(); $son = new Bio::Root::Object(-name => Junior, -parent => $dad, -make => full); See the new() method...


Platforms: *nix

Bio::Tree::Compatible is a Perl module for testing compatibility of phylogenetic trees with nested taxa. SYNOPSIS use Bio::Tree::Compatible; use Bio::TreeIO; my $input = new Bio::TreeIO(-format => newick, -file => input.tre); my $t1 = $input->next_tree; my $t2 = $input->next_tree; my...


Platforms: *nix

vnstat PHP frontend project is a PHP fronted end to vnStat, a network traffic logger. Since vnStat is console mode only I created this script to make a nice report of the data collected by vnStat. This script requires a working PHP setup with GD image libraries. Also vnStat must be properly...


Platforms: *nix

PHP Web Toolkit provides a rapid development toolkit for multi-layered Web applications written in PHP 5. The PHP Web Toolkit enables the rapid development of multi-layered Web applications and is designed to be easy to use, extensible, reliable, reusable, scalable, and secure. It integrates...


Platforms: *nix

Bio::TreeIO::svggraph is a simple output format that converts a Tree object to an SVG output. SYNOPSIS use Bio::TreeIO; my $in = new Bio::TreeIO(-file => input, -format => newick); my $out = new Bio::TreeIO(-file => >output, -format => svggraph); while( my $tree = $in->next_tree ) { my...


Platforms: *nix

php-sqlite3 project is a PHP extension that lets you access SQLite3 databases within your scripts. PHP 4 and PHP 5 have already built-in support for this RDBM, but this is limited to the 2.x releases. This extension adds support for SQLite 3.x release. Please note that this project is still...


Platforms: *nix

LinPHA is an easy to use, multilingual, flexible photo/image archive/album/gallery written in PHP. It uses a SQL database to store information about your pictures. It comes with a HTML based installer, so you dont need experience in setting up SQL DB..


Platforms: *nix