Erica Hill Bio
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 (97): Bio::Tools::Run::PiseWorkflow 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 (97): Bio::NEXUS::Block Download |
Bio::Factory::SeqAnalysisParserFactoryI is a Perl interface describing objects capable of creating SeqAnalysisParserI compliant parsers. SYNOPSIS # initialize an object implementing this interface, e.g. $factory = Bio::Factory::SeqAnalysisParserFactory->new(); # obtain a parser object...
Platforms: *nix
License: Freeware | Size: 4.7 MB | Download (97): Bio::Factory::SeqAnalysisParserFactoryI Download |
Bio::Index::Blast is a Perl module with indexes Blast reports and supports retrieval based on query accession(s). SYNOPSIS use strict; use Bio::Index::Blast; my ($indexfile,$file1, $file2); my $index = new Bio::Index::Blast(-filename => $indexfile, -write_flag => 1);...
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License: Freeware | Size: 4.7 MB | Download (97): Bio::Index::Blast Download |
Bio::Phylo::IO Perl module contains input and output of phylogenetic data. SYNOPSIS use Bio::Phylo::IO; # parsing a tree from a newick string my $tree_string = (((A,B),C),D);; my $tree = Bio::Phylo::IO->parse( -string => $tree_string, # old parser, always adds node labels -format =>...
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License: Freeware | Size: 143.36 KB | Download (97): Bio::Phylo::IO 0.17 Download |
Bio::Biblio::Patent is a representation of a patent. SYNOPSIS $obj = new Bio::Biblio::Patent (-doc_number => 1-2-3-4-5); #--- OR --- $obj = new Bio::Biblio::Patent; $obj->doc_number (1-2-3-4-5); A storage object for a patent. See its place in the class hierarchy in...
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License: Freeware | Size: 4.7 MB | Download (96): Bio::Biblio::Patent Download |
Bio::Tools::Run::JavaRunner is a Perl module that can run java programs. SYNOPSIS my $runner = Bio::Tools::Run::JavaRunner->new(-jar => $jar); $runner->run(); This module is probably incomplete. It is intended to be a wrapper for running java programs..
Platforms: *nix
License: Freeware | Size: 942.08 KB | Download (96): Bio::Tools::Run::JavaRunner Download |
Bio::AlignIO::msf is a Perl module with msf sequence input/output stream. SYNOPSIS Do not use this module directly. Use it via the Bio::AlignIO class. This object can transform Bio::Align::AlignI objects to and from msf flat file databases. The rest of the documentation details each of...
Platforms: *nix
License: Freeware | Size: 4.7 MB | Download (96): Bio::AlignIO::msf Download |
Bio::Network::IO::dip_tab is a Perl class for parsing interaction data in DIP tab-delimited format. SYNOPSIS Do not use this module directly, use Bio::Network::IO. For example: my $io = Bio::Network::IO->new(-format => dip_tab, -file => data.dip); my $network = $io->next_network; The...
Platforms: *nix
License: Freeware | Size: 99.33 KB | Download (96): Bio::Network::IO::dip_tab Download |
Bio::NEXUS::DistancesBlock is a Perl module that represents DISTANCES block in NEXUS file. The DistancesBlock class represents a NEXUS Distances Block and provides methods for reading, writing, and accessing data within these blocks. Distances Blocks contain distance matrices, or a table of...
Platforms: *nix
License: Freeware | Size: 153.6 KB | Download (96): Bio::NEXUS::DistancesBlock Download |
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 (95): Bio::Tools::Run::PiseApplication::align2model 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::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::Tree::DistanceFactory is a Perl module to construct a tree using distance based methods. SYNOPSIS use Bio::Tree::DistanceFactory; use Bio::AlignIO; use Bio::Align::DNAStatistics; my $tfactory = Bio::Tree::DistanceFactory->new(-method => "NJ"); my $stats =...
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License: Freeware | Size: 5.6 MB | Download (95): Bio::Tree::DistanceFactory Download |
Bio::Graphics::Glyph::cds module contains the "cds" glyph. SYNOPSIS See L< Bio::Graphics::Panel > and L< Bio::Graphics::Glyph >. This glyph draws features that are associated with a protein coding region. At high magnifications, draws a series of boxes that are color-coded to indicate the...
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License: Freeware | Size: 4.7 MB | Download (95): Bio::Graphics::Glyph::cds 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...
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License: Freeware | Size: 5.6 MB | Download (94): Bio::Tree::Compatible Download |
Bio::Tools::Run::PiseApplication::freak is a Perl module. Bio::Tools::Run::PiseApplication::freak Bioperl class for: FREAK Residue/base frequency table or plot (EMBOSS) Parameters: (see also: http://bioweb.pasteur.fr/seqanal/interfaces/freak.html for available values): freak...
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License: Freeware | Size: 829.44 KB | Download (94): Bio::Tools::Run::PiseApplication::freak Download |
A deserted mansion on the hill suddenly came alive! It's Halloween and all the restless creatures of the night are on a wild rampage. Vampire bats circling in the air are looking for prey, Jack O' Lanterns have gone crazy and there is some kind of odd celebration going on inside. Will you dare...
Platforms: Windows
License: Shareware | Cost: $19.95 USD | Size: 9.55 KB | Download (94): 3D Haunted Halloween Screensaver 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::ConnectDots::SimpleGraph is a simple, hopefully fast undirected graph package. SYNOPSIS use SimpleGraph; my $graph=new Bio::ConnectDots::SimpleGraph; # read pairs of nodes from STDIN while (<>) { my($node1,$node2)=split; $graph->add_edge($node1,$node2); } my @nodes=graph->nodes;...
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License: Freeware | Size: 102.4 KB | Download (93): Bio::ConnectDots::SimpleGraph Download |