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Erica Hill Bio software
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Erica Hill Bio

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Added: March 15, 2010 | Visits: 1.729

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 (97): Bio::Tools::Run::PiseWorkflow Download

Added: February 19, 2010 | Visits: 1.195

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 (97): Bio::NEXUS::Block Download

Added: January 27, 2010 | Visits: 988

Bio::Factory::SeqAnalysisParserFactoryI 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

Added: January 21, 2010 | Visits: 1.470

Bio::Index::Blast 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);... Platforms: *nix

License: Freeware Size: 4.7 MB Download (97): Bio::Index::Blast Download

Added: June 19, 2010 | Visits: 708

Bio::Phylo::IO 0.17 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 =>... Platforms: *nix

License: Freeware Size: 143.36 KB Download (97): Bio::Phylo::IO 0.17 Download

Added: November 05, 2010 | Visits: 647

Bio::Biblio::Patent 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... Platforms: *nix

License: Freeware Size: 4.7 MB Download (96): Bio::Biblio::Patent Download

Added: March 16, 2010 | Visits: 777

Bio::Tools::Run::JavaRunner 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

Added: August 13, 2010 | Visits: 774

Bio::AlignIO::msf 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

Added: August 01, 2010 | Visits: 940

Bio::Network::IO::dip_tab 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

Added: July 08, 2010 | Visits: 914

Bio::NEXUS::DistancesBlock 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

Added: August 02, 2010 | Visits: 1.816

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

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Added: July 21, 2010 | Visits: 729

Bio::Ontology::GOterm 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

Added: April 10, 2010 | Visits: 724

Bio::AnnotationCollectionI 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

Added: November 22, 2010 | Visits: 893

Bio::Tree::DistanceFactory 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 =... Platforms: *nix

License: Freeware Size: 5.6 MB Download (95): Bio::Tree::DistanceFactory Download

Added: April 03, 2010 | Visits: 1.173

Bio::Graphics::Glyph::cds 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... Platforms: *nix

License: Freeware Size: 4.7 MB Download (95): Bio::Graphics::Glyph::cds Download

Added: November 26, 2010 | Visits: 1.234

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 (94): Bio::Tree::Compatible Download

Added: November 23, 2010 | Visits: 1.184

Bio::Tools::Run::PiseApplication::freak 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... Platforms: *nix

License: Freeware Size: 829.44 KB Download (94): Bio::Tools::Run::PiseApplication::freak Download

Added: August 17, 2008 | Visits: 1.078

3D Haunted Halloween Screensaver 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

Added: October 11, 2010 | Visits: 881

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.... Platforms: *nix

License: Freeware Size: 153.6 KB Download (93): Bio::NEXUS::TaxaBlock Download

Added: April 08, 2010 | Visits: 657

Bio::ConnectDots::SimpleGraph 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;... Platforms: *nix

License: Freeware Size: 102.4 KB Download (93): Bio::ConnectDots::SimpleGraph Download

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