|
Bio::AssemblyImprovement
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::AssemblyImprovement::Abacas::DelimiterRole
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::AssemblyImprovement::Abacas::Iterative
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::AssemblyImprovement::Abacas::Main
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::AssemblyImprovement::AdapterRemoval::Trimmomatic::Main
|
AJPAGE
|
SSJUNNEBO
VOFFFORD
|
|
Bio::AssemblyImprovement::Assemble::SGA::IndexAndCorrectReads
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::AssemblyImprovement::Assemble::SGA::Main
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::AssemblyImprovement::Assemble::SGA::PreprocessReads
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::AssemblyImprovement::Circlator::Main
|
AJPAGE
|
SSJUNNEBO
VOFFFORD
|
|
Bio::AssemblyImprovement::DigitalNormalisation::Khmer::Main
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::AssemblyImprovement::FillGaps::GapFiller::Config
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::AssemblyImprovement::FillGaps::GapFiller::Iterative
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::AssemblyImprovement::FillGaps::GapFiller::Main
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::AssemblyImprovement::IvaQC::Main
|
AJPAGE
|
SSJUNNEBO
VOFFFORD
|
|
Bio::AssemblyImprovement::PrepareForSubmission::RenameContigs
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::AssemblyImprovement::PrimerRemoval::Main
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::AssemblyImprovement::Quiver::Main
|
AJPAGE
|
SSJUNNEBO
VOFFFORD
|
|
Bio::AssemblyImprovement::Scaffold::Descaffold
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::AssemblyImprovement::Scaffold::SSpace::Config
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::AssemblyImprovement::Scaffold::SSpace::Iterative
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::AssemblyImprovement::Scaffold::SSpace::Main
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::AssemblyImprovement::Scaffold::SSpace::OutputFilenameRole
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::AssemblyImprovement::Scaffold::SSpace::PreprocessInputFiles
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::AssemblyImprovement::Scaffold::SSpace::TempDirectoryRole
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::AssemblyImprovement::Util::FastaTools
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::AssemblyImprovement::Util::FastqCleanupRole
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::AssemblyImprovement::Util::FastqTools
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::AssemblyImprovement::Util::GetReadLengthsRole
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::AssemblyImprovement::Util::OrderContigsByLength
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::AssemblyImprovement::Util::UnzipFileIfNeededRole
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::AssemblyImprovement::Util::ZipFileRole
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::AssemblyImprovement::Validate::Executable
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::MLST::Blast::BlastN
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::MLST::Blast::Database
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::MLST::CDC::Convert
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::MLST::Check
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::MLST::CheckMultipleSpecies
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::MLST::CompareAlleles
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::MLST::DatabaseSettings
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::MLST::Databases
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::MLST::Download::Database
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::MLST::Download::Databases
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::MLST::Download::Downloadable
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::MLST::Exceptions
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::MLST::FilterAlleles
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::MLST::NormaliseFasta
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::MLST::OutputFasta
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::MLST::ProcessFasta
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::MLST::SearchForFiles
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::MLST::SequenceType
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::MLST::Spreadsheet::File
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::MLST::Spreadsheet::Row
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::MLST::Types
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::MLST::Validate::Executable
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::MLST::Validate::File
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::MLST::Validate::Resource
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::Roary
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::Roary::AccessoryBinaryFasta
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::Roary::AccessoryClustering
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::Roary::AnalyseGroups
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::Roary::AnnotateGroups
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::Roary::AssemblyStatistics
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::Roary::BedFromGFFRole
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::Roary::ChunkFastaFile
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::Roary::ClustersRole
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::Roary::CombinedProteome
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::Roary::CommandLine::AssemblyStatistics
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::Roary::CommandLine::Common
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::Roary::CommandLine::CreatePanGenome
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::Roary::CommandLine::ExtractProteomeFromGff
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::Roary::CommandLine::GeneAlignmentFromNucleotides
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::Roary::CommandLine::IterativeCdhit
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::Roary::CommandLine::MergeMultipleFastaAlignments
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::Roary::CommandLine::ParallelAllAgainstAllBlastp
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::Roary::CommandLine::ProteinMuscleAlignmentFromNucleotides
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::Roary::CommandLine::QueryRoary
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::Roary::CommandLine::Roary
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::Roary::CommandLine::RoaryCoreAlignment
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::Roary::CommandLine::RoaryPostAnalysis
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::Roary::CommandLine::RoaryReorderSpreadsheet
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::Roary::CommandLine::TransferAnnotationToGroups
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::Roary::CommandLine::UniqueGenesPerSample
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::Roary::ContigsToGeneIDsFromGFF
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::Roary::Exceptions
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::Roary::External::Blastp
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::Roary::External::Cdhit
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::Roary::External::CheckTools
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::Roary::External::Fasttree
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::Roary::External::GeneAlignmentFromNucleotides
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::Roary::External::IterativeCdhit
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::Roary::External::Mafft
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::Roary::External::Makeblastdb
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::Roary::External::Mcl
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::Roary::External::Muscle
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::Roary::External::PostAnalysis
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::Roary::External::Prank
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::Roary::External::ProteinMuscleAlignmentFromNucleotides
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::Roary::External::Revtrans
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::Roary::External::Segmasker
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::Roary::ExtractCoreGenesFromSpreadsheet
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::Roary::ExtractProteomeFromGFF
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::Roary::ExtractProteomeFromGFFs
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::Roary::FilterFullClusters
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::Roary::FilterUnknownsFromFasta
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::Roary::GeneNamesFromGFF
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::Roary::GroupLabels
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::Roary::GroupStatistics
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::Roary::InflateClusters
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::Roary::IterativeCdhit
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::Roary::JobRunner::LSF
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::Roary::JobRunner::Local
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::Roary::JobRunner::Parallel
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::Roary::JobRunner::Role
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::Roary::LookupGeneFiles
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::Roary::MergeMultifastaAlignments
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::Roary::OrderGenes
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::Roary::Output::BlastIdentityFrequency
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::Roary::Output::CoreGeneAlignmentCoordinatesEMBL
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::Roary::Output::DifferenceBetweenSets
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::Roary::Output::EMBLHeaderCommon
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::Roary::Output::EmblGroups
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::Roary::Output::GroupMultifasta
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::Roary::Output::GroupsMultifastaNucleotide
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::Roary::Output::GroupsMultifastaProtein
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::Roary::Output::GroupsMultifastas
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::Roary::Output::GroupsMultifastasNucleotide
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::Roary::Output::NumberOfGroups
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::Roary::Output::QueryGroups
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::Roary::ParallelAllAgainstAllBlast
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::Roary::ParseGFFAnnotationRole
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::Roary::PostAnalysis
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::Roary::PrepareInputFiles
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::Roary::PresenceAbsenceMatrix
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::Roary::QC::Kraken
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::Roary::QC::Report
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::Roary::QC::ShredAssemblies
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::Roary::ReformatInputGFFs
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::Roary::ReorderSpreadsheet
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::Roary::SampleOrder
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::Roary::SequenceLengths
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::Roary::SortFasta
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::Roary::SplitGroups
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::Roary::SpreadsheetRole
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::Roary::UniqueGenesPerSample
|
AJPAGE
|
BEWT
SSJUNNEBO
VOFFFORD
|
|
Bio::Tradis
|
AJPAGE
|
BEWT
CARLAC
SSJUNNEBO
|
|
Bio::Tradis::AddTagsToSeq
|
AJPAGE
|
BEWT
CARLAC
PUETHE
SSJUNNEBO
|
|
Bio::Tradis::Analysis::Exceptions
|
AJPAGE
|
BEWT
CARLAC
PUETHE
SSJUNNEBO
|
|
Bio::Tradis::Analysis::InsertSite
|
AJPAGE
|
BEWT
CARLAC
PUETHE
SSJUNNEBO
|
|
Bio::Tradis::CombinePlots
|
AJPAGE
|
BEWT
CARLAC
PUETHE
SSJUNNEBO
VOFFFORD
|
|
Bio::Tradis::CommandLine::AddTags
|
AJPAGE
|
BEWT
CARLAC
PUETHE
SSJUNNEBO
|
|
Bio::Tradis::CommandLine::CheckTags
|
AJPAGE
|
BEWT
CARLAC
PUETHE
SSJUNNEBO
|
|
Bio::Tradis::CommandLine::FilterFastqTags
|
AJPAGE
|
BEWT
CARLAC
PUETHE
SSJUNNEBO
|
|
Bio::Tradis::CommandLine::PlotCombine
|
AJPAGE
|
BEWT
CARLAC
PUETHE
SSJUNNEBO
VOFFFORD
|
|
Bio::Tradis::CommandLine::PlotTradis
|
AJPAGE
|
BEWT
CARLAC
PUETHE
SSJUNNEBO
|
|
Bio::Tradis::CommandLine::RemoveFastqTags
|
AJPAGE
|
BEWT
CARLAC
PUETHE
SSJUNNEBO
|
|
Bio::Tradis::CommandLine::RunMapping
|
AJPAGE
|
BEWT
CARLAC
PUETHE
SSJUNNEBO
|
|
Bio::Tradis::CommandLine::TradisAnalysis
|
AJPAGE
|
BEWT
CARLAC
PUETHE
SSJUNNEBO
|
|
Bio::Tradis::CommandLine::TradisBam
|
AJPAGE
|
BEWT
CARLAC
PUETHE
SSJUNNEBO
|
|
Bio::Tradis::DetectTags
|
AJPAGE
|
BEWT
CARLAC
PUETHE
SSJUNNEBO
|
|
Bio::Tradis::Exception
|
AJPAGE
|
BEWT
CARLAC
PUETHE
SSJUNNEBO
VOFFFORD
|
|
Bio::Tradis::FilterTags
|
AJPAGE
|
BEWT
CARLAC
PUETHE
SSJUNNEBO
|
|
Bio::Tradis::Map
|
AJPAGE
|
BEWT
CARLAC
PUETHE
SSJUNNEBO
|
|
Bio::Tradis::Parser::Bam
|
AJPAGE
|
BEWT
CARLAC
PUETHE
SSJUNNEBO
|
|
Bio::Tradis::Parser::Cigar
|
AJPAGE
|
BEWT
CARLAC
PUETHE
SSJUNNEBO
VOFFFORD
|
|
Bio::Tradis::Parser::Fastq
|
AJPAGE
|
BEWT
CARLAC
PUETHE
SSJUNNEBO
|
|
Bio::Tradis::RemoveTags
|
AJPAGE
|
BEWT
CARLAC
PUETHE
SSJUNNEBO
|
|
Bio::Tradis::RunTradis
|
AJPAGE
|
BEWT
CARLAC
PUETHE
SSJUNNEBO
|
|
Bio::Tradis::Samtools
|
AJPAGE
|
BEWT
CARLAC
PUETHE
SSJUNNEBO
VOFFFORD
|
|
Bio::Tradis::TradisPlot
|
AJPAGE
|
BEWT
CARLAC
PUETHE
SSJUNNEBO
|