Documentation for bio (2.0.5)

Alphabetic Index

File Listing

README

Namespace Listing A-Z

AA (Bio::Sequence)
AAindex (Bio)
AAindex1 (Bio)
AAindex2 (Bio)
ANISOU (Bio::PDB::Record)
ATOM (Bio::PDB::Record)
Abif (Bio)
Acc2hit (Bio::Hinv)
AccessWait (Bio::TogoWS)
ActsLikeMap (Bio::Map)
ActsLikeMarker (Bio::Map)
Adapter (Bio::Sequence)
AlignedStrands (Bio::RestrictionEnzyme::DoubleStranded)
Alignment (Bio)
AlwaysNil (Bio::Blast::Default::Report)
AminoAcid (Bio)
AminoFormatter (Bio::Sequence::Format)
Analysis (Bio::RestrictionEnzyme)
Annotation (Bio::FANTOM::MaXML)
Annotations (Bio::FANTOM::MaXML)
ArrayExtension (Bio::Alignment)
AtomFinder (Bio::PDB)
AutoDetect (Bio::FlatFile)

BDBMappingFile (Bio::FlatFileIndex::BDB_1)
BDB_1 (Bio::FlatFileIndex)
BDBdefault (Bio::FlatFileIndex)
BDBwrapper (Bio::FlatFileIndex)
BRITE (Bio::KEGG)
BackwardCompatibility (Bio::Features)
BackwardCompatibility (Bio::References)
Baseml (Bio::PAML)
Bin (Bio::RestrictionEnzyme::Range::SequenceRange)
Bio
Bl2seq (Bio::Blast)
Blast (Bio)
BlastDefaultParser (Bio::FlatFileIndex::Indexer::Parser)
BlastXmlSplitter (Bio::Blast::Report)
Blat (Bio)
BufferedInputStream (Bio::FlatFile)
Buried (Bio::ColorScheme)

CELL (Bio::TRANSFAC)
CGIDriver (Bio::PSORT)
CLASS (Bio::TRANSFAC)
COMPOUND (Bio::KEGG)
CalculatedCuts (Bio::RestrictionEnzyme::Range::SequenceRange)
Chain (Bio::PDB)
ChainFinder (Bio::PDB)
CharactersBlock (Bio::Nexus)
ChemicalComponent (Bio::PDB)
ClustalW (Bio)
Cluster (Bio::FANTOM::MaXML)
Code (Bio::GFF::GFF3::Record::Gap)
Codeml (Bio::PAML)
CodonTable (Bio)
ColorScheme (Bio)
Command (Bio)
Common (Bio::EMBLDB)
Common (Bio::Hinv)
Common (Bio::Sequence)
Common (Bio::KEGG)
Common (Bio::PAML)
Common (Bio::NCBIDB)
Consensus (Bio::ColorScheme)
ConstLikeMethod (Bio::PDB::DataType)
ContingencyTable (Bio)
Converter (Bio::Sequence::QualityScore)
Coordinate (Bio::PDB)
CutLocationPair (Bio::RestrictionEnzyme::DoubleStranded)
CutLocationPairInEnzymeNotation (Bio::RestrictionEnzyme::DoubleStranded)
CutLocations (Bio::RestrictionEnzyme::DoubleStranded)
CutLocationsInEnzymeNotation (Bio::RestrictionEnzyme::SingleStrand)
CutLocationsInEnzymeNotation (Bio::RestrictionEnzyme::DoubleStranded)
CutRange (Bio::RestrictionEnzyme::Range)
CutRanges (Bio::RestrictionEnzyme::Range)
CutSymbol (Bio::RestrictionEnzyme)
CutSymbol__ (Bio::RestrictionEnzyme::CutSymbol)

DAS (Bio)
DB (Bio::KEGG::Keggtab)
DB (Bio::Registry)
DB (Bio)
DBLink (Bio::Sequence)
DDBJ (Bio)
DEBUG (Bio::FlatFileIndex)
DNA (Bio::DAS)
DRUG (Bio::KEGG)
DSN (Bio::DAS)
Data (Bio::NucleicAcid)
Data (Bio::AminoAcid)
DataBank (Bio::FlatFileIndex)
DataBlock (Bio::Nexus)
DataSrc (Bio::FANTOM::MaXML::Annotation)
DataType (Bio::PDB)
Database (Bio::SOFT)
Dataset (Bio::SOFT)
DblinksAsHash (Bio::KEGG::Common)
Default (Bio::Blast)
Default (Bio::FlatFile::Splitter)
DenseIntArray (Bio::RestrictionEnzyme)
Diff_ids (Bio::Fastq::Error)
DirectoryEntry (Bio::Abif)
DiseasesAsHash (Bio::KEGG::Common)
DisplayFragment (Bio::RestrictionEnzyme::Range::SequenceRange::Fragment)
DisplayFragment (Bio::RestrictionEnzyme::Range::SequenceRange::Fragments)
DistanceMatrix (Bio::Phylip)
DistancesBlock (Bio::Nexus)
DoubleStranded (Bio::RestrictionEnzyme)
DynamicMethod_Hash (Bio::REBASE)

EBI (Bio::Fetch)
EFetch (Bio::NCBI::REST)
EMBL (Bio::Sequence::Adapter)
EMBL (Bio)
EMBLDB (Bio)
EMBLParser (Bio::FlatFileIndex::Indexer::Parser)
EMBOSS (Bio)
ENTRY_POINT (Bio::DAS)
ENZYME (Bio::KEGG)
ESearch (Bio::NCBI::REST)
EXPRESSION (Bio::KEGG)
Edge (Bio::Tree)
Embl (Bio::Sequence::Format::NucFormatter)
Entity (Bio::SOFT)
Entry (Bio::KEGG::KGML)
EnumerableExtension (Bio::Alignment)
EnzymeAction (Bio::RestrictionEnzyme::DoubleStranded)
EnzymeEntry (Bio::REBASE)
Error (Bio::Fastq)
Escape (Bio::GFF::GFF2)
Escape (Bio::GFF::GFF3)
Exon (Bio::Genscan::Report)
External2go (Bio::GO)

F0dbstat (Bio::Blast::Bl2seq::Report)
F0dbstat (Bio::Blast::Default::Report)
F0dbstat (Bio::Blast::WU::Report)
FACTOR (Bio::TRANSFAC)
FANTOM (Bio)
FASTQ_ILLUMINA (Bio::Fastq::FormatData)
FASTQ_SANGER (Bio::Fastq::FormatData)
FASTQ_SOLEXA (Bio::Fastq::FormatData)
FEATURE (Bio::DAS)
FactoryTemplate (Bio::Alignment)
Fasta (Bio::Sequence::Format::Formatter)
Fasta (Bio)
FastaDefline (Bio)
FastaFormat (Bio)
FastaFormat (Bio::Sequence::Adapter)
FastaFormat10Splitter (Bio::Fasta::Report)
FastaFormatParser (Bio::FlatFileIndex::Indexer::Parser)
FastaNumericFormat (Bio)
FastaNumericFormat (Bio::Sequence::Adapter)
Fasta_ncbi (Bio::Sequence::Format::Formatter)
Fasta_numeric (Bio::Sequence::Format::Formatter)
Fastacmd (Bio::Blast)
Fastq (Bio::Sequence::Format::Formatter)
Fastq (Bio)
Fastq (Bio::Sequence::Adapter)
Fastq_illumina (Bio::Sequence::Format::Formatter)
Fastq_solexa (Bio::Sequence::Format::Formatter)
Feature (Bio)
Features (Bio)
Fetch (Bio)
FileID (Bio::FlatFileIndex)
FileIDs (Bio::FlatFileIndex)
FileInFileOut (Bio::Alignment::FactoryTemplate)
FileInFileOutWithTree (Bio::Alignment::FactoryTemplate)
FileInStdoutOut (Bio::Alignment::FactoryTemplate)
FlatFile (Bio)
FlatFileIndex (Bio)
FlatMappingFile (Bio::FlatFileIndex::Flat_1)
Flat_1 (Bio::FlatFileIndex)
Format (Bio::Sequence)
FormatData (Bio::Fastq)
Formatter (Bio::Sequence::Format)
FormatterBase (Bio::Sequence::Format)
Fragment (Bio::RestrictionEnzyme::Range::SequenceRange)
Fragment (Bio::RestrictionEnzyme)
Fragments (Bio::RestrictionEnzyme::Range::SequenceRange)
Fragments (Bio::RestrictionEnzyme)

GAP (Bio::Alignment)
GCG (Bio)
GENE (Bio::TRANSFAC)
GENES (Bio::KEGG)
GENOME (Bio::KEGG)
GFF (Bio::DAS)
GFF (Bio)
GFF2 (Bio::GFF)
GFF3 (Bio::GFF)
GLYCAN (Bio::KEGG)
GO (Bio)
GROUP (Bio::DAS)
Gap (Bio::GFF::GFF3::Record)
GenBank (Bio::Sequence::Adapter)
GenBank (Bio)
GenBankParser (Bio::FlatFileIndex::Indexer::Parser)
GenPept (Bio)
GenPeptParser (Bio::FlatFileIndex::Indexer::Parser)
Genbank (Bio::Sequence::Format::NucFormatter)
Gene (Bio::Genscan::Report)
GeneAssociation (Bio::GO)
Generic (Bio::Sequence)
GenericBlock (Bio::Nexus)
GenesAsHash (Bio::KEGG::Common)
GenomeNet (Bio::Blast::Remote)
Genscan (Bio)
Graphics (Bio::KEGG::KGML)

HETATM (Bio::PDB::Record)
HMMER (Bio)
HSP (Bio::Blast::Bl2seq::Report)
HSP (Bio::Blast::WU::Report)
HSP (Bio::Blast::Default::Report)
HashExtension (Bio::Alignment)
Header (Bio::SOFT::Table)
Helix (Bio::ColorScheme)
HetatmFinder (Bio::PDB)
Heterogen (Bio::PDB)
HeterogenFinder (Bio::PDB)
Hinv (Bio)
Hit (Bio::HMMER::Report)
Hit (Bio::Blast::Report)
Hit (Bio::Blast::Bl2seq::Report)
Hit (Bio::Blat::Report)
Hit (Bio::Blast::WU::Report)
Hit (Bio::Blast::Default::Report)
Hit (Bio::Fasta::Report)
Hit (Bio::Spidey::Report)
Hit (Bio::Sim4::Report)
Hit2acc (Bio::Hinv)
HitCnt (Bio::Hinv)
HitDefinition (Bio::Hinv)
HitPubmedId (Bio::Hinv)
HitXML (Bio::Hinv)
Hix2hit (Bio::Hinv)
HixCnt (Bio::Hinv)
HixRepresent (Bio::Hinv)
HixXML (Bio::Hinv)
HorizontalCutRange (Bio::RestrictionEnzyme::Range)
Hsp (Bio::HMMER::Report)
Hsp (Bio::Blast::Report)
Hydropathy (Bio::ColorScheme)

INSDFeatureHelper (Bio::Sequence::Format)
IPSORT (Bio::PSORT)
IdSearch (Bio::Hinv)
Indexer (Bio::FlatFileIndex)
Information (Bio::Blast::Remote)
Information (Bio::Blast::Remote::GenomeNet)
Iprscan (Bio)
Iteration (Bio::Blast::Default::Report)
Iteration (Bio::Blast::Report)
Iteration (Bio::Blast::Bl2seq::Report)
Iteration (Bio::Blast::WU::Report)
Iteration (Bio::Blast::RPSBlast::Report)

Jrnl (Bio::PDB::Record)

KEGG (Bio)
KEGGDB (Bio)
KGML (Bio::KEGG)
Keggtab (Bio::KEGG)
KeywordSearch (Bio::Hinv)

LINK (Bio::DAS)
LITDB (Bio)
Lasergene (Bio)
LineOriented (Bio::FlatFile::Splitter)
Location (Bio)
Locations (Bio)
Locus (Bio::GenBank)
Locus (Bio::GenPept)
Long_qual (Bio::Fastq::Error)

MAFFT (Bio)
MATRIX (Bio::TRANSFAC)
MEDLINE (Bio)
MODULE (Bio::KEGG)
MaXML (Bio::FANTOM)
MaXMLClusterParser (Bio::FlatFileIndex::Indexer::Parser)
MaXMLSequenceParser (Bio::FlatFileIndex::Indexer::Parser)
Map (Bio)
Mapping (Bio::Map)
Marker (Bio::Map)
Mast (Bio::Meme)
Match (Bio::Iprscan::Report)
Meme (Bio)
MetaData (Bio::GFF::GFF2)
Methods (Bio::NCBI::REST::EFetch)
Methods (Bio::NCBI::REST::ESearch)
Model (Bio::PDB)
Model (Bio::PAML::Codeml)
ModelFinder (Bio::PDB)
ModulesAsHash (Bio::KEGG::Common)
Motif (Bio::Meme)
Msf (Bio::GCG)
MultiFastaFormat (Bio::Alignment)
Muscle (Bio)
MutableRange (Bio::RestrictionEnzyme::DenseIntArray)

NA (Bio::Sequence)
NBRF (Bio)
NCBI (Bio)
NCBIDB (Bio)
NCBIOptions (Bio::Blast)
NameSpace (Bio::FlatFileIndex::Template)
NameSpace (Bio::FlatFileIndex::Indexer)
NameSpaces (Bio::FlatFileIndex)
NameSpaces (Bio::FlatFileIndex::Indexer)
Newick (Bio)
Nexus (Bio)
NexusMatrix (Bio::Nexus)
NexusMatrixError (Bio::Nexus::NexusMatrix)
NexusParseError (Bio::Nexus)
NoPathError (Bio::Tree)
No_atmark (Bio::Fastq::Error)
No_ids (Bio::Fastq::Error)
No_qual (Bio::Fastq::Error)
No_seq (Bio::Fastq::Error)
Node (Bio::Tree)
NucFormatter (Bio::Sequence::Format)
NucleicAcid (Bio)
Nucleotide (Bio::ColorScheme)

ORTHOLOGY (Bio::KEGG)
Ontology (Bio::GO)
OriginalAlignment (Bio::Alignment)
OriginalPrivate (Bio::Alignment)
OrthologsAsHash (Bio::KEGG::Common)
Output (Bio::Alignment)

PAML (Bio)
PATHWAY (Bio::KEGG)
PDB (Bio)
PDBChemicalComponentParser (Bio::FlatFileIndex::Indexer::Parser)
PROSITE (Bio)
PSORT (Bio)
PSORT1 (Bio::PSORT)
PSORT2 (Bio::PSORT)
PSORTB (Bio::PSORT)
PTS1 (Bio)
Pair (Bio::SiRNA)
ParseError (Bio::Newick)
Parser (Bio::FlatFileIndex::Indexer)
Pathway (Bio)
PathwaysAsHash (Bio::KEGG::Common)
Pdb_Integer (Bio::PDB::DataType)
Pdb_LString (Bio::PDB::DataType)
Pdb_List (Bio::PDB::DataType)
Pdb_Real (Bio::PDB::DataType)
Pdb_SList (Bio::PDB::DataType)
Pdb_Specification_list (Bio::PDB::DataType)
Pdb_String (Bio::PDB::DataType)
Pdb_StringRJ (Bio::PDB::DataType)
Phred (Bio::Sequence::QualityScore)
Phylip (Bio)
PhylipFormat (Bio::Phylip)
Platform (Bio::SOFT)
PositiveSite (Bio::PAML::Codeml)
PositiveSites (Bio::PAML::Codeml)
PrimaryNameSpace (Bio::FlatFileIndex::Flat_1)
PrimaryNameSpace (Bio::FlatFileIndex::BDB_1)
Probcons (Bio)
Product (Bio::KEGG::KGML)
Program (Bio::Fasta::Report)
PropertyMethods (Bio::Alignment)
PubMed (Bio)

Qual (Bio::Sequence::Format::Formatter)
Qual_char (Bio::Fastq::Error)
Qual_range (Bio::Fastq::Error)
Qualifier (Bio::Feature)
QualityScore (Bio::Sequence)
Query (Bio::Fasta::Report::Hit)

REACTION (Bio::KEGG)
REBASE (Bio)
REST (Bio::NCBI)
REST (Bio::TogoWS)
RPSBlast (Bio::Blast)
RPSBlastSplitter (Bio::Blast::RPSBlast)
Range (Bio::RestrictionEnzyme)
Rates (Bio::PAML::Codeml)
Raw (Bio::Sequence::Format::Formatter)
Reaction (Bio::KEGG::KGML)
Record (Bio::FlatFileIndex::Flat_1)
Record (Bio::PDB)
Record (Bio::PDB::ChemicalComponent)
Record (Bio::GFF::GFF3)
Record (Bio::GFF)
Record (Bio::GFF::GFF2)
RecordBoundary (Bio::GFF::GFF3)
RefSeq (Bio)
Reference (Bio)
References (Bio)
References (Bio::KEGG::Common)
Registry (Bio)
Relation (Bio::KEGG::KGML)
Relation (Bio)
Remark1 (Bio::PDB::Record)
Remark2 (Bio::PDB::Record)
Remote (Bio::Blast)
Remote (Bio::PSORT::PSORT1)
Remote (Bio::PSORT::PSORT2)
Remover (Bio::Command::Tmpdir)
Report (Bio::TMHMM)
Report (Bio::SOSUI)
Report (Bio::PSORT::PSORT2)
Report (Bio::MAFFT)
Report (Bio::PSORT::PSORT1)
Report (Bio::HMMER)
Report (Bio::Blast)
Report (Bio::Blat)
Report (Bio::Sim4)
Report (Bio::PTS1)
Report (Bio::PAML::Common)
Report (Bio::PAML::Codeml)
Report (Bio::PAML::Baseml)
Report (Bio::PAML::Yn00)
Report (Bio::Meme::Mast)
Report (Bio::ClustalW)
Report (Bio::TargetP)
Report (Bio::Genscan)
Report (Bio::Iprscan)
Report (Bio::Fasta)
Report (Bio::Blast::RPSBlast)
Report (Bio::Spidey)
Report (Bio::Blast::WU)
Report (Bio::Blast::Default)
Report (Bio::Blast::Bl2seq)
ReportError (Bio::PAML::Codeml)
ReportSingle (Bio::PAML::Codeml)
Report_TBlast (Bio::Blast::WU)
Report_TBlast (Bio::Blast::Default)
Report_tab (Bio::Blast)
Residue (Bio::PDB)
ResidueFinder (Bio::PDB)
RestrictionEnzyme (Bio)
Result (Bio::RestrictionEnzyme::DoubleStranded::AlignedStrands)
Results (Bio::FlatFileIndex)
Row (Bio::SOFT::Table)
RuleDebug (Bio::FlatFile::AutoDetect)
RuleProc (Bio::FlatFile::AutoDetect)
RuleRegexp (Bio::FlatFile::AutoDetect)
RuleRegexp2 (Bio::FlatFile::AutoDetect)
RuleSpecial (Bio::FlatFile::AutoDetect)
RuleTemplate (Bio::FlatFile::AutoDetect)
RulesArray (Bio::FlatFile::AutoDetect)

SEGMENT (Bio::DAS)
SEQUENCE (Bio::DAS)
SITE (Bio::TRANSFAC)
SOFT (Bio)
SOSUI (Bio)
SPTRParser (Bio::FlatFileIndex::Indexer::Parser)
Sample (Bio::SOFT)
Samples (Bio::SOFT)
SangerChromatogram (Bio)
SangerChromatogram (Bio::Sequence::Adapter)
Scf (Bio)
Score (Bio::ColorScheme)
SecondaryNameSpace (Bio::FlatFileIndex::Flat_1)
SecondaryNameSpace (Bio::FlatFileIndex::BDB_1)
Segment (Bio::Sim4::Report)
Segment (Bio::Spidey::Report)
SegmentPair (Bio::Sim4::Report)
SegmentPair (Bio::Blat::Report)
SegmentPair (Bio::Spidey::Report)
Seq (Bio::GCG)
SeqDesc (Bio::Blat::Report)
SeqDesc (Bio::Sim4::Report)
SeqDesc (Bio::Spidey::Report)
Seq_char (Bio::Fastq::Error)
Sequence (Bio::FANTOM::MaXML)
Sequence (Bio)
SequenceArray (Bio::Alignment)
SequenceHash (Bio::Alignment)
SequenceMasker (Bio::Sequence)
SequenceRange (Bio::RestrictionEnzyme::Range)
SequenceRegion (Bio::GFF::GFF3)
Sequences (Bio::FANTOM::MaXML)
Series (Bio::SOFT)
ShRNA (Bio::SiRNA)
Short_qual (Bio::Fastq::Error)
SiRNA (Bio)
Sim4 (Bio)
Simple (Bio::ColorScheme)
Simple (Bio::Alignment::FactoryTemplate)
SimpleMap (Bio::Map)
SingleStrand (Bio::RestrictionEnzyme)
SingleStrandComplement (Bio::RestrictionEnzyme)
Site (Bio::Alignment)
SiteMethods (Bio::Alignment)
Skipped_unformatted_lines (Bio::Fastq::Error)
Solexa (Bio::Sequence::QualityScore)
SortedNumArray (Bio::RestrictionEnzyme)
Spidey (Bio)
Splitter (Bio::FlatFile)
StdinInFileOut (Bio::Alignment::FactoryTemplate)
Strand (Bio::ColorScheme)
StringFormatting (Bio::RestrictionEnzyme)
StringsAsHash (Bio::KEGG::Common)
Subset (Bio::SOFT)
Subsets (Bio::SOFT)
Substrate (Bio::KEGG::KGML)
SubstrateProduct (Bio::KEGG::KGML)
SwissProt (Bio)

TARGET (Bio::DAS)
TMH (Bio::SOSUI::Report)
TMH (Bio::TMHMM)
TMHMM (Bio)
TRANSFAC (Bio)
TYPE (Bio::DAS)
TYPES (Bio::DAS)
Table (Bio::SOFT)
Target (Bio::Fasta::Report::Hit)
Target (Bio::GFF::GFF3::Record)
TargetP (Bio)
TaxaBlock (Bio::Nexus)
Taylor (Bio::ColorScheme)
Tcoffee (Bio)
Template (Bio::FlatFile::Splitter)
Template (Bio::FlatFileIndex)
TemplateParser (Bio::FlatFileIndex::Indexer::Parser)
Tmpdir (Bio::Command)
TogoWS (Bio)
TrEMBL (Bio)
Tree (Bio)
TreesBlock (Bio::Nexus)
Turn (Bio::ColorScheme)

UniProtKB (Bio)
UnknownDataFormatError (Bio::FlatFile)
Util (Bio::Nexus)
Utils (Bio::PDB)

Value (Bio::GFF::GFF2::Record)
VerticalCutRange (Bio::RestrictionEnzyme::Range)

WU (Bio::Blast)
WoLF_PSORT (Bio::PSORT)
WrapInputStdin (Bio::Alignment::FactoryTemplate)
WrapInputTempfile (Bio::Alignment::FactoryTemplate)
WrapOutputStdout (Bio::Alignment::FactoryTemplate)
WrapOutputTempfile (Bio::Alignment::FactoryTemplate)

Yn00 (Bio::PAML)

Zappo (Bio::ColorScheme)