roary (3.13.0+dfsg-2build1)
2 versions available in ubuntu/resolute/universe/riscv64
Details
Core information at a glance
- Distribution
- ubuntu
- Origin
- ubuntu-resolute-ports
- Repository
- https://ports.ubuntu.com
- Codename
- resolute
- Component
- universe
- Source
- roary
- Architecture
- riscv64
- Section
- universe/science
- Priority
- extra
- Maintainer
- Ubuntu Developers <[email protected]>
Size & integrity
Byte sizes and integrity verification
- Installed size
- 738.3 kB
- Size expected
- 179.8 kB
- Size actual
- 179.8 kB
- Size match
- match
Dependencies
Required package dependencies
- 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
Recommends
Recommended package dependencies
- None
Suggested packages
Recommended additional packages
- None
Provides
Virtual packages provided
- None
Description
high speed stand alone pan genome pipeline
Tags
Package classification tags
None
Checksums
Hash values and integrity verification status
| Type | Actual | Match |
|---|---|---|
| MD5 | bb07f4ff…f744e531 | not available |
| SHA-1 | 52c69222…cdba9cde | not available |
| SHA-256 | 92550b64…ff52aea9 | not available |
| SHA-512 | 4c1595f4…2ff47c85 | match |
Contents
Files and directories included
. usr usr/bin 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 usr/share/doc usr/share/doc/roary usr/share/doc/roary/README.test usr/share/doc/roary/changelog.Debian.gz usr/share/doc/roary/copyright usr/share/doc/roary/examples 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 usr/share/man/man1 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 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 usr/share/perl5/Bio usr/share/perl5/Bio/Roary 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 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 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 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 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 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 usr/share/perl5/Bio/Roary.pm
Versions
2 versions in this repository slot, newest first