Hunter Patch Adams Bio

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....

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...

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

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

KPowersave Icon Patch is intended for KPowersave 0.6.2 This patch changes the way of displaying power state for KPowersave. Using this patch you can better theme KPowersave, by using a series of pixmaps. Installation instructions: >>> Patch the sources 1. Copy the patch file in the parent...


Platforms: *nix

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

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

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

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

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

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

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

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

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

kwin dropshadow patch for kde is the well known KDE KWin dropshadow patch ported to KDE Version 3.5.7, but it may apply to all 3.5.x Versions (untested!) For all ATI users and those whose laptops are too slow for real composite (like mine is).. kwin dropshadow patch for kde 3.5.7 KDE-Apps.org...


Platforms: *nix

OpenSSH LDAP Public Key patch provides an easy way of centralizing strong user authentication by using an LDAP server for retrieving public keys instead of ~/.ssh/authorized_keys. It uses the standard core.schema/nis.schema and strongAuthenticationUser object class, which can simplify login...


Platforms: *nix

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

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

Bio::PrimarySeqI is a Perl Interface definition for a Bio::PrimarySeq. SYNOPSIS # Bio::PrimarySeqI is the interface class for sequences. # If you are a newcomer to bioperl, you should # start with Bio::Seq documentation. This # documentation is mainly for developers using # Bioperl. #...


Platforms: *nix