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Platforms: Windows
License: Shareware | Cost: $14.95 USD | Size: 1.21 MB | Download (139): Recycle Bin Manager Download |
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 (99): Bio::Graphics::Glyph::alignment Download |
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 (86): Bio::OntologyIO::simplehierarchy Download |
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 (213): Bio::Tools::Run::TribeMCL Download |
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 (91): Bio::NEXUS::Block Download |
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
License: Freeware | Size: 153.6 KB | Download (98): Bio::NEXUS::Node Download |
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
License: Freeware | Size: 153.6 KB | Download (93): Bio::NEXUS::TaxaBlock Download |
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 (91): Bio::NEXUS::TreesBlock Download |
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 (141): Bio::Restriction::Enzyme Download |
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
License: Freeware | Size: 4.7 MB | Download (96): Bio::Root::Object Download |
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 = $input->next_tree; my...
Platforms: *nix
License: Freeware | Size: 5.6 MB | Download (94): Bio::Tree::Compatible Download |
Bio::Tools::Run::PiseApplication::fasta is a Bioperl class for sequence database search. Parameters: fasta (Excl) Fasta program query (Sequence) Query sequence File pipe: seqfile seqtype (Excl) Is it a DNA or protein sequence (-n) protein_db (Excl) Protein Database nucleotid_db...
Platforms: *nix
License: Freeware | Size: 82.94 KB | Download (101): Bio::Tools::Run::PiseApplication::fasta Download |
Bio::Tools::Run::PiseApplication::consensus is a Perl module. Bioperl class for: CONSENSUS Identification of consensus patterns in unaligned DNA and protein sequences (Hertz, Stormo) References: G.Z. Hertz and G.D. Stormo. Identification of consensus patterns in unaligned DNA and protein...
Platforms: *nix
License: Freeware | Size: 829.44 KB | Download (100): Bio::Tools::Run::PiseApplication::consensus Download |
Bio::NEXUS::WeightSet is a Perl module that represents column weights in alignment ( for each character). SYNOPSIS new Bio::NEXUS::WeightSet($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 (89): Bio::NEXUS::WeightSet Download |
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...
Platforms: *nix
License: Freeware | Size: 153.6 KB | Download (99): Bio::NEXUS::HistoryBlock Download |
Bio::Ontology::Relationship is a relationship for an ontology. SYNOPSIS $rel = Bio::Ontology::Relationship->new( -identifier => "16847", -subject_term => $subj, -object_term => $obj, -predicate_term => $pred ); This is a basic implementation of Bio::Ontology::RelationshipI. The...
Platforms: *nix
License: Freeware | Size: 4.7 MB | Download (109): Bio::Ontology::Relationship Download |
Bio::Ontology::GOterm is a representation of GO terms. SYNOPSIS $term = Bio::Ontology::GOterm->new ( -go_id => "GO:0016847", -name => "1-aminocyclopropane-1-carboxylate synthase", -definition => "Catalysis of ...", -is_obsolete => 0, -comment => "" ); $term->add_definition_references(...
Platforms: *nix
License: Freeware | Size: 4.7 MB | Download (95): Bio::Ontology::GOterm Download |
Bio::ConnectDots::ConnectDots is a top level class for connect-the-dots. SYNOPSIS use Bio::ConnectDots::DB; use Bio::ConnectDots::ConnectDots; my $db=new Bio::ConnectDots::DB(-database=>test, -host=>computername, -user=>usename, -password=>secret); my $cd=my $cd=new...
Platforms: *nix
License: Freeware | Size: 102.4 KB | Download (98): Bio::ConnectDots::ConnectDots Download |
Bio::AnnotationCollectionI is a Perl interface for annotation collections. SYNOPSIS # get an AnnotationCollectionI somehow, eg $ac = $seq->annotation(); foreach $key ( $ac->get_all_annotation_keys() ) { @values = $ac->get_Annotations($key); foreach $value ( @values ) { # value is an...
Platforms: *nix
License: Freeware | Size: 4.7 MB | Download (95): Bio::AnnotationCollectionI Download |
Bio::Seq is a sequence object, with features. SYNOPSIS # This is the main sequence object in Bioperl # gets a sequence from a file $seqio = Bio::SeqIO->new( -format => embl , -file => myfile.dat); $seqobj = $seqio->next_seq(); # SeqIO can both read and write sequences; see Bio::SeqIO #...
Platforms: *nix
License: Freeware | Size: 4.7 MB | Download (98): Bio::Seq Download |