roary (3.13.0+dfsg-2)

Details

Core information at a glance

Distribution: kali
Origin: kali-rolling
Repository: https://http.kali.org/kali
Codename: kali-rolling
Component: main
Source: none
Architecture: i386
Section: science
Priority: optional
Maintainer: Debian Med Packaging Team <[email protected]>

Size & integrity

Byte sizes and integrity verification

Installed size: 732 B
Size expected: 185.4 kB
Size actual: 185.4 kB
Size 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

Suggested packages

Recommended additional packages

None

Description

high speed stand alone pan genome pipeline

Homepage Download .deb

Checksums

Hash values and integrity verification status

Type	Expected	Actual
MD5	b9a06082…3f644c54	b9a06082…3f644c54
SHA-1	15c0daf3…cd9a92f3	15c0daf3…cd9a92f3
SHA-256	d17eb667…152cd648	d17eb667…152cd648
SHA-512	Not provided	81f05319…10e08c3b

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/changelog.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