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Bio Freeze Equipment software
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Bio Freeze Equipment

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Added: January 18, 2010 | Visits: 724

Bio::Tree::NodeNHX Bio::Tree::NodeNHX is a Simple Tree Node with support for NHX tags. SYNOPSIS use Bio::Tree::NodeNHX; my $nodeA = new Bio::Tree::NodeNHX(); my $nodeL = new Bio::Tree::NodeNHX(); my $nodeR = new Bio::Tree::NodeNHX(); my $node = new Bio::Tree::NodeNHX(); $node->add_Descendents($nodeL);...



Platforms: *nix

License: Freeware Size: 4.7 MB Download (94): Bio::Tree::NodeNHX Download

Added: January 24, 2010 | Visits: 1.259

Bio::Graphics::Glyph::alignment Bio::Graphics::Glyph::alignment is the "alignment" glyph. SYNOPSIS See L< Bio::Graphics::Panel > and L< Bio::Graphics::Glyph >. This is identical to the "graded_segments" glyph, and is used for drawing features that consist of discontinuous segments. The color intensity of each segment is...





Platforms: *nix

License: Freeware Size: 4.7 MB Download (77): Bio::Graphics::Glyph::alignment Download

Added: April 02, 2010 | Visits: 564

Bio::OntologyIO::simplehierarchy 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",...


Platforms: *nix

License: Freeware Size: 4.7 MB Download (70): Bio::OntologyIO::simplehierarchy Download

Added: March 15, 2010 | Visits: 1.113

Bio::Tools::Run::PiseWorkflow 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

License: Freeware Size: 829.44 KB Download (73): Bio::Tools::Run::PiseWorkflow Download

Added: January 14, 2010 | Visits: 804

Bio::Tools::AlignFactory 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

License: Freeware Size: 4.7 MB Download (138): Bio::Tools::AlignFactory Download

Added: March 27, 2010 | Visits: 1.133

Bio::Tools::Run::TribeMCL 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

License: Freeware Size: 829.44 KB Download (168): Bio::Tools::Run::TribeMCL Download

Added: February 19, 2010 | Visits: 733

Bio::NEXUS::Block 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

License: Freeware Size: 153.6 KB Download (71): Bio::NEXUS::Block Download

Added: November 27, 2010 | Visits: 907

Bio::NEXUS::Node 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...


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License: Freeware Size: 153.6 KB Download (75): Bio::NEXUS::Node Download

Added: October 11, 2010 | Visits: 597

Bio::NEXUS::TaxaBlock 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....


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License: Freeware Size: 153.6 KB Download (73): Bio::NEXUS::TaxaBlock Download

Added: May 21, 2010 | Visits: 629

Bio::NEXUS::TreesBlock 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

License: Freeware Size: 153.6 KB Download (70): Bio::NEXUS::TreesBlock Download

Added: August 26, 2010 | Visits: 1.048

Bio::Restriction::Enzyme 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

License: Freeware Size: 4.7 MB Download (111): Bio::Restriction::Enzyme Download

Added: September 24, 2010 | Visits: 625

Bio::Root::Object 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...


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License: Freeware Size: 4.7 MB Download (73): Bio::Root::Object Download

Added: November 26, 2010 | Visits: 815

Bio::Tree::Compatible 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

License: Freeware Size: 5.6 MB Download (77): Bio::Tree::Compatible Download

Added: November 05, 2010 | Visits: 658

Bio::TreeIO::svggraph 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

License: Freeware Size: 4.7 MB Download (75): Bio::TreeIO::svggraph Download

Added: October 24, 2010 | Visits: 985

Bio::Tools::Run::PiseApplication::fasta Bio::Tools::Run::PiseApplication::fasta is a Bioperl class for sequence database search. Parameters: fasta (Excl) Fasta program query (Sequence) Query sequence File pipe: seqfile seqtype (Excl) Is it a DNA or protein sequence (-n) protein_db (Excl) Protein Database nucleotid_db...


Platforms: *nix

License: Freeware Size: 82.94 KB Download (79): Bio::Tools::Run::PiseApplication::fasta Download

Added: August 02, 2010 | Visits: 1.225

Bio::Tools::Run::PiseApplication::align2model Bio::Tools::Run::PiseApplication::align2model is a Bioperl class for align2model - create a multiple alignment of sequences to an existing model. Parameters: align2model (String) run (String) Run name db (Sequence) Sequences to align (-db) model_file (InFile) Model (-i) pipe:...


Platforms: *nix

License: Freeware Size: 829.44 KB Download (75): Bio::Tools::Run::PiseApplication::align2model Download

Added: January 07, 2010 | Visits: 1.258

Bio::Tools::Run::PiseApplication::consensus Bio::Tools::Run::PiseApplication::consensus is a Perl module. Bioperl class for: CONSENSUS Identification of consensus patterns in unaligned DNA and protein sequences (Hertz, Stormo) References: G.Z. Hertz and G.D. Stormo. Identification of consensus patterns in unaligned DNA and protein...


Platforms: *nix

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Added: October 23, 2010 | Visits: 1.624

Bio::Tools::Run::PiseApplication::charge Bio::Tools::Run::PiseApplication::charge is a Perl module. Bio::Tools::Run::PiseApplication::charge Bioperl class for: CHARGE Protein charge plot (EMBOSS) Parameters: (see also: http://bioweb.pasteur.fr/seqanal/interfaces/charge.html for available values): charge (String) init...


Platforms: *nix

License: Freeware Size: 829.44 KB Download (72): Bio::Tools::Run::PiseApplication::charge Download

Added: September 12, 2010 | Visits: 630

Bio::NEXUS::WeightSet Bio::NEXUS::WeightSet is a Perl module that represents column weights in alignment ( for each character). SYNOPSIS new Bio::NEXUS::WeightSet($name, @weights, $iswt); A module representing column weights in alignment (for each character) METHODS new Title : new Usage : $node = new...


Platforms: *nix

License: Freeware Size: 153.6 KB Download (73): Bio::NEXUS::WeightSet Download

Added: August 02, 2010 | Visits: 592

Bio::NEXUS::HistoryBlock Bio::NEXUS::HistoryBlock is a Perl module that represents a HISTORY block of a NEXUS file. SYNOPSIS $block_object = new Bio::NEXUS::HistoryBlock(history, $block, $verbose); This is a class representing a history block in NEXUS file METHODS new Title : new Usage : block_object = new...


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License: Freeware Size: 153.6 KB Download (83): Bio::NEXUS::HistoryBlock Download

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