Package - roary

Primary informations

Download package: http://deb.debian.org/debian/pool/main/r/roary/roary_3.13.0+dfsg-2_all.deb (Size: 181.0KiB)

Property	Value
Package	roary
Version	3.13.0+dfsg-2
Installed-Size	732
Maintainer	Debian Med Packaging Team
Architecture	all
Depends	perl:any, bioperl (>= 1.7.4), libarray-utils-perl, libdigest-md5-file-perl, libenv-path-perl, libexception-class-perl, libfile-find-rule-perl, libfile-grep-perl, libfile-slurper-perl, libfile-which-perl, libfindbin-libs-perl, libgraph-perl, libgraph-readwrite-perl, liblog-log4perl-perl, libmoose-perl, libperlio-utf8-strict-perl, libtest-most-perl, libtest-file-perl, libtest-files-perl, libtest-output-perl, libtext-csv-perl, bedtools, cd-hit, ncbi-blast+, mcl, parallel, prank, r-base-core, r-cran-ggplot2, mafft, fasttree
Description	high speed stand alone pan genome pipeline
Description-md5	6d457fd706202fc2ef292eacf7b46029
Homepage	https://sanger-pathogens.github.io/Roary/
Tag	field::biology, field::biology:bioinformatics, implemented-in::perl, interface::commandline, role::program, scope::utility, use::analysing, use::comparing
Section	science
Priority	optional
Filename	pool/main/r/roary/roary_3.13.0+dfsg-2_all.deb
Size	185372
MD5sum	b9a0608203b4c68c800b0b143f644c54
SHA256	d17eb6670706c80adb047f608f299e09cad011f4d21f330036010db9152cd648

Files in package

• /usr/bin/create_pan_genome
• /usr/bin/create_pan_genome_plots
• /usr/bin/extract_proteome_from_gff
• /usr/bin/iterative_cdhit
• /usr/bin/pan_genome_assembly_statistics
• /usr/bin/pan_genome_core_alignment
• /usr/bin/pan_genome_post_analysis
• /usr/bin/pan_genome_reorder_spreadsheet
• /usr/bin/parallel_all_against_all_blastp
• /usr/bin/protein_alignment_from_nucleotides
• /usr/bin/query_pan_genome
• /usr/bin/roary
• /usr/bin/roary-create_pan_genome_plots
• /usr/bin/roary-pan_genome_reorder_spreadsheet
• /usr/bin/roary-query_pan_genome
• /usr/bin/roary-unique_genes_per_sample
• /usr/bin/transfer_annotation_to_groups
• /usr/share/doc/roary/README.test
• /usr/share/doc/roary/changelog.Debian.gz
• /usr/share/doc/roary/changelog.gz
• /usr/share/doc/roary/copyright
• /usr/share/doc/roary/examples/genbank1.gff
• /usr/share/doc/roary/examples/genbank1.gff.proteome.faa.expected
• /usr/share/doc/roary/examples/genbank2.gff
• /usr/share/doc/roary/examples/genbank2.gff.proteome.faa.expected
• /usr/share/doc/roary/examples/genbank3.gff
• /usr/share/doc/roary/examples/genbank3.gff.proteome.faa.expected
• /usr/share/doc/roary/examples/genbank_gene_presence_absence.csv
• /usr/share/doc/roary/expected_files.out
• /usr/share/doc/roary/run-unit-test
• /usr/share/man/man1/create_pan_genome.1p.gz
• /usr/share/man/man1/create_pan_genome_plots.1p.gz
• /usr/share/man/man1/extract_proteome_from_gff.1p.gz
• /usr/share/man/man1/iterative_cdhit.1p.gz
• /usr/share/man/man1/pan_genome_assembly_statistics.1p.gz
• /usr/share/man/man1/pan_genome_core_alignment.1p.gz
• /usr/share/man/man1/pan_genome_post_analysis.1p.gz
• /usr/share/man/man1/pan_genome_reorder_spreadsheet.1p.gz
• /usr/share/man/man1/parallel_all_against_all_blastp.1p.gz
• /usr/share/man/man1/protein_alignment_from_nucleotides.1p.gz
• /usr/share/man/man1/query_pan_genome.1p.gz
• /usr/share/man/man1/roary-pan_genome_reorder_spreadsheet.1p.gz
• /usr/share/man/man1/roary-query_pan_genome.1p.gz
• /usr/share/man/man1/roary-unique_genes_per_sample.1p.gz
• /usr/share/man/man1/roary.1p.gz
• /usr/share/man/man1/transfer_annotation_to_groups.1p.gz
• /usr/share/man/man3/Bio::Roary.3pm.gz
• /usr/share/man/man3/Bio::Roary::AccessoryBinaryFasta.3pm.gz
• /usr/share/man/man3/Bio::Roary::AccessoryClustering.3pm.gz
• /usr/share/man/man3/Bio::Roary::AnalyseGroups.3pm.gz
• /usr/share/man/man3/Bio::Roary::AnnotateGroups.3pm.gz
• /usr/share/man/man3/Bio::Roary::AssemblyStatistics.3pm.gz
• /usr/share/man/man3/Bio::Roary::BedFromGFFRole.3pm.gz
• /usr/share/man/man3/Bio::Roary::ChunkFastaFile.3pm.gz
• /usr/share/man/man3/Bio::Roary::ClustersRole.3pm.gz
• /usr/share/man/man3/Bio::Roary::CombinedProteome.3pm.gz
• /usr/share/man/man3/Bio::Roary::CommandLine::AssemblyStatistics.3pm.gz
• /usr/share/man/man3/Bio::Roary::CommandLine::Common.3pm.gz
• /usr/share/man/man3/Bio::Roary::CommandLine::CreatePanGenome.3pm.gz
• /usr/share/man/man3/Bio::Roary::CommandLine::ExtractProteomeFromGff.3pm.gz
• /usr/share/man/man3/Bio::Roary::CommandLine::GeneAlignmentFromNucleotides.3pm.gz
• /usr/share/man/man3/Bio::Roary::CommandLine::IterativeCdhit.3pm.gz
• /usr/share/man/man3/Bio::Roary::CommandLine::ParallelAllAgainstAllBlastp.3pm.gz
• /usr/share/man/man3/Bio::Roary::CommandLine::QueryRoary.3pm.gz
• /usr/share/man/man3/Bio::Roary::CommandLine::Roary.3pm.gz
• /usr/share/man/man3/Bio::Roary::CommandLine::RoaryCoreAlignment.3pm.gz
• /usr/share/man/man3/Bio::Roary::CommandLine::RoaryPostAnalysis.3pm.gz
• /usr/share/man/man3/Bio::Roary::CommandLine::RoaryReorderSpreadsheet.3pm.gz
• /usr/share/man/man3/Bio::Roary::CommandLine::TransferAnnotationToGroups.3pm.gz
• /usr/share/man/man3/Bio::Roary::CommandLine::UniqueGenesPerSample.3pm.gz
• /usr/share/man/man3/Bio::Roary::ContigsToGeneIDsFromGFF.3pm.gz
• /usr/share/man/man3/Bio::Roary::Exceptions.3pm.gz
• /usr/share/man/man3/Bio::Roary::External::Blastp.3pm.gz
• /usr/share/man/man3/Bio::Roary::External::Cdhit.3pm.gz
• /usr/share/man/man3/Bio::Roary::External::CheckTools.3pm.gz
• /usr/share/man/man3/Bio::Roary::External::Fasttree.3pm.gz
• /usr/share/man/man3/Bio::Roary::External::GeneAlignmentFromNucleotides.3pm.gz
• /usr/share/man/man3/Bio::Roary::External::IterativeCdhit.3pm.gz
• /usr/share/man/man3/Bio::Roary::External::Mafft.3pm.gz
• /usr/share/man/man3/Bio::Roary::External::Makeblastdb.3pm.gz
• /usr/share/man/man3/Bio::Roary::External::Mcl.3pm.gz
• /usr/share/man/man3/Bio::Roary::External::PostAnalysis.3pm.gz
• /usr/share/man/man3/Bio::Roary::External::Prank.3pm.gz
• /usr/share/man/man3/Bio::Roary::ExtractCoreGenesFromSpreadsheet.3pm.gz
• /usr/share/man/man3/Bio::Roary::ExtractProteomeFromGFF.3pm.gz
• /usr/share/man/man3/Bio::Roary::ExtractProteomeFromGFFs.3pm.gz
• /usr/share/man/man3/Bio::Roary::FilterFullClusters.3pm.gz
• /usr/share/man/man3/Bio::Roary::FilterUnknownsFromFasta.3pm.gz
• /usr/share/man/man3/Bio::Roary::GeneNamesFromGFF.3pm.gz
• /usr/share/man/man3/Bio::Roary::GroupLabels.3pm.gz
• /usr/share/man/man3/Bio::Roary::GroupStatistics.3pm.gz
• /usr/share/man/man3/Bio::Roary::InflateClusters.3pm.gz
• /usr/share/man/man3/Bio::Roary::IterativeCdhit.3pm.gz
• /usr/share/man/man3/Bio::Roary::JobRunner::Local.3pm.gz
• /usr/share/man/man3/Bio::Roary::JobRunner::Parallel.3pm.gz
• /usr/share/man/man3/Bio::Roary::JobRunner::Role.3pm.gz
• /usr/share/man/man3/Bio::Roary::LookupGeneFiles.3pm.gz
• /usr/share/man/man3/Bio::Roary::MergeMultifastaAlignments.3pm.gz
• /usr/share/man/man3/Bio::Roary::OrderGenes.3pm.gz
• /usr/share/man/man3/Bio::Roary::Output::BlastIdentityFrequency.3pm.gz
• /usr/share/man/man3/Bio::Roary::Output::CoreGeneAlignmentCoordinatesEMBL.3pm.gz
• /usr/share/man/man3/Bio::Roary::Output::DifferenceBetweenSets.3pm.gz
• /usr/share/man/man3/Bio::Roary::Output::EMBLHeaderCommon.3pm.gz
• /usr/share/man/man3/Bio::Roary::Output::EmblGroups.3pm.gz
• /usr/share/man/man3/Bio::Roary::Output::GroupMultifasta.3pm.gz
• /usr/share/man/man3/Bio::Roary::Output::GroupsMultifastaNucleotide.3pm.gz
• /usr/share/man/man3/Bio::Roary::Output::GroupsMultifastaProtein.3pm.gz
• /usr/share/man/man3/Bio::Roary::Output::GroupsMultifastas.3pm.gz
• /usr/share/man/man3/Bio::Roary::Output::GroupsMultifastasNucleotide.3pm.gz
• /usr/share/man/man3/Bio::Roary::Output::NumberOfGroups.3pm.gz
• /usr/share/man/man3/Bio::Roary::Output::QueryGroups.3pm.gz
• /usr/share/man/man3/Bio::Roary::ParallelAllAgainstAllBlast.3pm.gz
• /usr/share/man/man3/Bio::Roary::ParseGFFAnnotationRole.3pm.gz
• /usr/share/man/man3/Bio::Roary::PostAnalysis.3pm.gz
• /usr/share/man/man3/Bio::Roary::PrepareInputFiles.3pm.gz
• /usr/share/man/man3/Bio::Roary::PresenceAbsenceMatrix.3pm.gz
• /usr/share/man/man3/Bio::Roary::QC::Report.3pm.gz
• /usr/share/man/man3/Bio::Roary::ReformatInputGFFs.3pm.gz
• /usr/share/man/man3/Bio::Roary::ReorderSpreadsheet.3pm.gz
• /usr/share/man/man3/Bio::Roary::SampleOrder.3pm.gz
• /usr/share/man/man3/Bio::Roary::SequenceLengths.3pm.gz
• /usr/share/man/man3/Bio::Roary::SortFasta.3pm.gz
• /usr/share/man/man3/Bio::Roary::SplitGroups.3pm.gz
• /usr/share/man/man3/Bio::Roary::SpreadsheetRole.3pm.gz
• /usr/share/man/man3/Bio::Roary::UniqueGenesPerSample.3pm.gz
• /usr/share/perl5/Bio/Roary.pm
• /usr/share/perl5/Bio/Roary/AccessoryBinaryFasta.pm
• /usr/share/perl5/Bio/Roary/AccessoryClustering.pm
• /usr/share/perl5/Bio/Roary/AnalyseGroups.pm
• /usr/share/perl5/Bio/Roary/AnnotateGroups.pm
• /usr/share/perl5/Bio/Roary/AssemblyStatistics.pm
• /usr/share/perl5/Bio/Roary/BedFromGFFRole.pm
• /usr/share/perl5/Bio/Roary/ChunkFastaFile.pm
• /usr/share/perl5/Bio/Roary/ClustersRole.pm
• /usr/share/perl5/Bio/Roary/CombinedProteome.pm
• /usr/share/perl5/Bio/Roary/CommandLine/AssemblyStatistics.pm
• /usr/share/perl5/Bio/Roary/CommandLine/Common.pm
• /usr/share/perl5/Bio/Roary/CommandLine/CreatePanGenome.pm
• /usr/share/perl5/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm
• /usr/share/perl5/Bio/Roary/CommandLine/GeneAlignmentFromNucleotides.pm
• /usr/share/perl5/Bio/Roary/CommandLine/IterativeCdhit.pm
• /usr/share/perl5/Bio/Roary/CommandLine/ParallelAllAgainstAllBlastp.pm
• /usr/share/perl5/Bio/Roary/CommandLine/QueryRoary.pm
• /usr/share/perl5/Bio/Roary/CommandLine/Roary.pm
• /usr/share/perl5/Bio/Roary/CommandLine/RoaryCoreAlignment.pm
• /usr/share/perl5/Bio/Roary/CommandLine/RoaryPostAnalysis.pm
• /usr/share/perl5/Bio/Roary/CommandLine/RoaryReorderSpreadsheet.pm
• /usr/share/perl5/Bio/Roary/CommandLine/TransferAnnotationToGroups.pm
• /usr/share/perl5/Bio/Roary/CommandLine/UniqueGenesPerSample.pm
• /usr/share/perl5/Bio/Roary/ContigsToGeneIDsFromGFF.pm
• /usr/share/perl5/Bio/Roary/Exceptions.pm
• /usr/share/perl5/Bio/Roary/External/Blastp.pm
• /usr/share/perl5/Bio/Roary/External/Cdhit.pm
• /usr/share/perl5/Bio/Roary/External/CheckTools.pm
• /usr/share/perl5/Bio/Roary/External/Fasttree.pm
• /usr/share/perl5/Bio/Roary/External/GeneAlignmentFromNucleotides.pm
• /usr/share/perl5/Bio/Roary/External/IterativeCdhit.pm
• /usr/share/perl5/Bio/Roary/External/Mafft.pm
• /usr/share/perl5/Bio/Roary/External/Makeblastdb.pm
• /usr/share/perl5/Bio/Roary/External/Mcl.pm
• /usr/share/perl5/Bio/Roary/External/PostAnalysis.pm
• /usr/share/perl5/Bio/Roary/External/Prank.pm
• /usr/share/perl5/Bio/Roary/ExtractCoreGenesFromSpreadsheet.pm
• /usr/share/perl5/Bio/Roary/ExtractProteomeFromGFF.pm
• /usr/share/perl5/Bio/Roary/ExtractProteomeFromGFFs.pm
• /usr/share/perl5/Bio/Roary/FilterFullClusters.pm
• /usr/share/perl5/Bio/Roary/FilterUnknownsFromFasta.pm
• /usr/share/perl5/Bio/Roary/GeneNamesFromGFF.pm
• /usr/share/perl5/Bio/Roary/GroupLabels.pm
• /usr/share/perl5/Bio/Roary/GroupStatistics.pm
• /usr/share/perl5/Bio/Roary/InflateClusters.pm
• /usr/share/perl5/Bio/Roary/IterativeCdhit.pm
• /usr/share/perl5/Bio/Roary/JobRunner/Local.pm
• /usr/share/perl5/Bio/Roary/JobRunner/Parallel.pm
• /usr/share/perl5/Bio/Roary/JobRunner/Role.pm
• /usr/share/perl5/Bio/Roary/LookupGeneFiles.pm
• /usr/share/perl5/Bio/Roary/MergeMultifastaAlignments.pm
• /usr/share/perl5/Bio/Roary/OrderGenes.pm
• /usr/share/perl5/Bio/Roary/Output/BlastIdentityFrequency.pm
• /usr/share/perl5/Bio/Roary/Output/CoreGeneAlignmentCoordinatesEMBL.pm
• /usr/share/perl5/Bio/Roary/Output/DifferenceBetweenSets.pm
• /usr/share/perl5/Bio/Roary/Output/EMBLHeaderCommon.pm
• /usr/share/perl5/Bio/Roary/Output/EmblGroups.pm
• /usr/share/perl5/Bio/Roary/Output/GroupMultifasta.pm
• /usr/share/perl5/Bio/Roary/Output/GroupsMultifastaNucleotide.pm
• /usr/share/perl5/Bio/Roary/Output/GroupsMultifastaProtein.pm
• /usr/share/perl5/Bio/Roary/Output/GroupsMultifastas.pm
• /usr/share/perl5/Bio/Roary/Output/GroupsMultifastasNucleotide.pm
• /usr/share/perl5/Bio/Roary/Output/NumberOfGroups.pm
• /usr/share/perl5/Bio/Roary/Output/QueryGroups.pm
• /usr/share/perl5/Bio/Roary/ParallelAllAgainstAllBlast.pm
• /usr/share/perl5/Bio/Roary/ParseGFFAnnotationRole.pm
• /usr/share/perl5/Bio/Roary/PostAnalysis.pm
• /usr/share/perl5/Bio/Roary/PrepareInputFiles.pm
• /usr/share/perl5/Bio/Roary/PresenceAbsenceMatrix.pm
• /usr/share/perl5/Bio/Roary/QC/Report.pm
• /usr/share/perl5/Bio/Roary/ReformatInputGFFs.pm
• /usr/share/perl5/Bio/Roary/ReorderSpreadsheet.pm
• /usr/share/perl5/Bio/Roary/SampleOrder.pm
• /usr/share/perl5/Bio/Roary/SequenceLengths.pm
• /usr/share/perl5/Bio/Roary/SortFasta.pm
• /usr/share/perl5/Bio/Roary/SplitGroups.pm
• /usr/share/perl5/Bio/Roary/SpreadsheetRole.pm
• /usr/share/perl5/Bio/Roary/UniqueGenesPerSample.pm