section 1 · User commands 💻

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B (continued)

botch-fix-cross-problems(1)fix Packages files with the output of botch-cross-problems✨
botch-graph-ancestors(1)find all ancestors of a vertex in a graph in GraphML or dot format✨
botch-graph-descendants(1)find all descendants of a vertex in a graph in GraphML or dot format✨
botch-graph-difference(1)graph diff✨
botch-graph-info(1)show info about a buildgraph or sourcegraph✨
botch-graph-neighborhood(1)extract the neighborhood around a vertex✨
botch-graph-shortest-path(1)find the shortest path(s) between two vertices of a graph in GraphML or dot format✨
botch-graph-sinks(1)find all sinks (vertices without successors) in a graph in GraphML or dot format✨
botch-graph-sources(1)find all sources (vertices without predecessors) in a graph in GraphML or dot format✨
botch-graph-tred(1)find the transitive reduction of a graph in GraphML or dot format✨
botch-graph2text(1)for each vertex in a graph print a formatted line on standard output✨
botch-graphml2dot(1)converts graphml to dot✨
botch-latest-version(1)only keep the latest version✨
botch-ma-diff(1)diff two packages files for differences in their multiarch values✨
botch-multiarch-interpreter-problem(1)find all arch:all packages that allow switching architectures✨
botch-native(1)execute botch tools in the native phase✨
botch-optuniv(1)self contained repository with minimal number of source packages✨
botch-packages-diff(1)create a diff between two Packages or Sources files✨
botch-packages-difference(1)calculate the asymmetric set difference✨
botch-packages-intersection(1)calculate the set intersection✨
botch-packages-union(1)calculate the set union✨
botch-partial-order(1)calculate the partial vertex order✨
botch-print-stats(1)find cycles, selfcycles, amount of cycles through edges, feedback arc and vertex set, strong articulation points and bridges✨
botch-profile-build-fvs(1)remove droppable dependencies from graph✨
botch-remove-virtual-disjunctions(1)remove virtual dependency disjunctions✨
botch-src2bin(1)turn source packages into their binary packages✨
botch-stat-html(1)turn the JSON output of botch-print-stats into human readable HTML✨
botch-transition(1)calculate a transition order✨
botch-wanna-build-sortblockers(1)importance of source packages for ports✨
botch-y-u-b-d-transitive-essential(1)Find out why source packages are B-D transitive essential.✨
botch-y-u-no-bootstrap(1)Find out why Debian cannot be bootstrapped.✨
botsay(1)a utility for outputting text with an ASCII art robot✨
botti(1)Run an irssi module, such as a bot, without a UI✨
bottle(1)command line interface✨
bound(1)Find boundary numbers in files or STDIN.✨
boundaryFoam(1)part of OpenFOAM (The Open Source CFD Toolbox).✨
bower(1)✨
bowtie(1)ultrafast memory-efficient short read aligner✨
bowtie-build(1)building a colorspace index for bowtie✨
bowtie-build-debug(1)building a colorspace index for bowtie✨
bowtie-debug(1)ultrafast memory-efficient short read aligner✨
bowtie-inspect(1)extracts information from a bowtie index✨
bowtie-inspect-debug(1)extracts information from a bowtie index✨
bowtie2(1)wrapper for bowtie2-align-*✨
bowtie2-align-l(1)ultrafast and memory-efficient backend tool for aligning sequencing reads to long reference sequences✨
bowtie2-align-s(1)ultrafast and memory-efficient backend tool for aligning sequencing reads to long reference sequences✨
bowtie2-build(1)wrapper for bowtie2-build-*✨
bowtie2-build-l(1)building a colorspace index for bowtie2✨
bowtie2-build-s(1)building a colorspace index for bowtie2✨
bowtie2-inspect(1)wrapper for bowtie2-inspect-* index✨
bowtie2-inspect-l(1)extracts information from a bowtie2 index✨
bowtie2-inspect-s(1)extracts information from a bowtie2 index✨
box64(1)Linux Userspace x86_64 Emulator with a twist✨
boxer(1p)boxer command line utils✨
boxes(1)text mode box and comment drawing filter✨
boxshade(1)Pretty-printing of multiple sequence alignments✨
boxsym-rnd(1)generate box shaped symbol(s)✨
boxTurb(1)part of OpenFOAM (The Open Source CFD Toolbox).✨
bp-analyze(1)Generate an HTML report summarizing bali-phy runs.✨
bp4dbg(1)ADIOS2 utility✨
bp5dbg(1)ADIOS2 utility✨
bp_aacomp(1)amino acid composition of protein sequences✨
bp_aacomp(1p)amino acid composition of protein sequences✨
bp_biblio(1p)bioperl client for accessing and querying a bibliographic repository✨
bp_biofetch_genbank_proxy(1p)Caching BioFetch-compatible web proxy for GenBank✨
bp_bioflat_index(1)index sequence files using Bio::DB::Flat✨
bp_bioflat_index(1p)index sequence files using Bio::DB::Flat✨
bp_biogetseq(1)sequence retrieval using OBDA registry✨
bp_biogetseq(1p)sequence retrieval using OBDA registry✨
bp_bulk_load_gff(1p)Bulk-load a Bio::DB::GFF database from GFF files.✨
bp_dbsplit(1)script to split an input set of database(s) into smaller pieces✨
bp_dbsplit(1p)script to split an input set of database(s) into smaller pieces✨
bp_download_query_genbank(1p)script to query Genbank and retrieve records✨
bp_einfo(1p)Query einfo to find all available databases or information about a specific database (field information or links to other NCBI databases).✨
bp_extract_feature_seq(1)extract the corresponding sequence for a specified feature type✨
bp_extract_feature_seq(1p)extract the corresponding sequence for a specified feature type✨
bp_fast_load_gff(1p)Fast-load a Bio::DB::GFF database from GFF files.✨
bp_fastam9_to_table(1)turn FASTA -m 9 output into NCBI -m 9 tabular output✨
bp_fastam9_to_table(1p)turn FASTA -m 9 output into NCBI -m 9 tabular output✨
bp_fetch(1)fetches sequences from bioperl indexed databases✨
bp_fetch(1p)fetches sequences from bioperl indexed databases✨
bp_filter_search(1)filters searchio results, outputting a tab delimited summary✨
bp_filter_search(1p)filters searchio results, outputting a tab delimited summary✨
bp_find-blast-matches(1)extract DNA sequences based on BLAST hits✨
bp_find-blast-matches(1p)extract DNA sequences based on BLAST hits✨
bp_flanks(1p)finding flanking sequences for a variant in a sequence position✨
bp_gccalc(1)GC content of nucleotide sequences✨
bp_gccalc(1p)GC content of nucleotide sequences✨
bp_genbank2gff(1p)Load a Bio::DB::GFF database from GENBANK files.✨
bp_genbank2gff3(1)Genbank->gbrowse-friendly GFF3✨
bp_genbank2gff3(1p)Genbank->gbrowse-friendly GFF3✨
bp_genbank_ref_extractor(1p)Retrieves all related sequences for a list of searches on Entrez gene✨
bp_generate_histogram(1p)Generate a histogram of Bio::DB::GFF features✨
bp_hmmer_to_table.pl(1p)turn HMMER output into tabular format✨
bp_index(1)indexes files for use by bp_fetch.pl✨
bp_index(1p)indexes files for use by bp_fetch.pl✨
bp_load_gff(1p)Load a Bio::DB::GFF database from GFF files.✨
bp_local_taxonomydb_query(1)query a local TaxonomyDB for species or taxonid✨
bp_local_taxonomydb_query(1p)query a local TaxonomyDB for species or taxonid✨
bp_make_mrna_protein(1)Convert an input mRNA/cDNA sequence into protein✨
bp_make_mrna_protein(1p)Convert an input mRNA/cDNA sequence into protein✨
bp_mask_by_search(1)mask sequence(s) based on its alignment results✨
bp_mask_by_search(1p)mask sequence(s) based on its alignment results✨
bp_meta_gff(1p)Get/set Bio::DB::GFF meta-data✨
bp_mrtrans(1)implement a transformer of alignments from protein to mrna coordinates✨
bp_mrtrans(1p)implement a transformer of alignments from protein to mrna coordinates✨
bp_multi_hmmsearch.pl(1p)perform a hmmsearch into multiple FASTA files using an INDEX file✨
bp_mutate(1)randomly mutagenize a single protein or DNA sequence✨
bp_mutate(1p)randomly mutagenize a single protein or DNA sequence✨
bp_nexus2nh(1)convert nexus format trees (from PAUP* and MrBayes) to new hampshire✨
bp_nexus2nh(1p)convert nexus format trees (from PAUP* and MrBayes) to new hampshire✨
bp_nrdb(1)a script to emulate Warren Gish's nrdb, make a unique sequence database from a set of input databases✨
bp_nrdb(1p)a script to emulate Warren Gish's nrdb, make a unique sequence database from a set of input databases✨
bp_oligo_count(1)oligo count and frequency✨
bp_oligo_count(1p)oligo count and frequency✨
bp_pairwise_kaks(1p)calculate pairwise Ka,Ks for a set of sequences✨
bp_panalysis.pl(1p)An example/tutorial script how to access analysis tools✨
bp_papplmaker.pl(1p)Analysis tools module generator✨
bp_parse_hmmsearch.pl(1p)parse single/multiple HMMSEARCH results file(s) with different output options✨
bp_process_gadfly(1)Massage Gadfly/FlyBase GFF files into a version suitable for the Generic Genome Browser✨
bp_process_gadfly(1p)Massage Gadfly/FlyBase GFF files into a version suitable for the Generic Genome Browser✨
bp_process_sgd(1)Massage SGD annotation flat files into a version suitable for the Generic Genome Browser✨
bp_process_sgd(1p)Massage SGD annotation flat files into a version suitable for the Generic Genome Browser✨
bp_process_wormbase.pl(1p)Massage WormBase GFF files into a version suitable for the Generic Genome Browser✨
bp_query_entrez_taxa(1p)query Entrez taxonomy database and print out information✨
bp_remote_blast.pl(1p)script for submitting jobs to a remote blast server (ncbi blast queue at this time)✨
bp_revtrans-motif(1)Reverse translate a Profam-like protein motif✨
bp_revtrans-motif(1p)Reverse translate a Profam-like protein motif✨
bp_run_neighbor.pl(1p)run Phylip's 'neighbor' program through Bioperl✨
bp_run_protdist.pl(1p)run Phylip's 'protdist' program through Bioperl✨
bp_search2alnblocks(1)Turn SearchIO parseable reports(s) into a set of aligned blocks✨
bp_search2alnblocks(1p)Turn SearchIO parseable reports(s) into a set of aligned blocks✨
bp_search2gff(1)turn a SearchIO report into GFF✨
bp_search2gff(1p)turn a SearchIO report into GFF✨
bp_search2table(1)turn SearchIO parseable reports into tab delimited format like NCBI's -m 9✨
bp_search2table(1p)turn SearchIO parseable reports into tab delimited format like NCBI's -m 9✨
bp_search2tribe(1)Turn SearchIO parseable reports(s) into TRIBE matrix✨
bp_search2tribe(1p)Turn SearchIO parseable reports(s) into TRIBE matrix✨
bp_seq_length(1)lists the number of bases and number of sequences in specified sequence database files✨
bp_seq_length(1p)lists the number of bases and number of sequences in specified sequence database files✨
bp_seqconvert(1)generic BioPerl sequence format converter✨
bp_seqconvert(1p)generic BioPerl sequence format converter✨
bp_seqcut(1)cut FASTA sequences with a given range✨
bp_seqcut(1p)cut FASTA sequences with a given range✨
bp_seqfeature_load(1p)Load GFF into a SeqFeature database✨
bp_seqpart(1)Takes one or more sequence files and splits them into a number of load balanced files.✨
bp_seqpart(1p)Takes one or more sequence files and splits them into a number of load balanced files.✨
bp_seqret(1)bioperl implementation of sequence fetch from local db (like EMBOSS seqret)✨
bp_seqret(1p)bioperl implementation of sequence fetch from local db (like EMBOSS seqret)✨
bp_seqretsplit(1)split a sequence (or stream) into a single file per sequence✨
bp_seqretsplit(1p)split a sequence (or stream) into a single file per sequence✨
bp_split_seq(1)splits a sequence into equal sized chunks with an optional overlapping range✨
bp_split_seq(1p)splits a sequence into equal sized chunks with an optional overlapping range✨
bp_sreformat(1)convert sequence formats✨
bp_sreformat(1p)convert sequence formats✨
bp_taxid4species(1)simple script which returns the NCBI Taxonomic id for a requested species✨
bp_taxid4species(1p)simple script which returns the NCBI Taxonomic id for a requested species✨
bp_taxonomy2tree(1)Building a taxonomic tree based on the full lineages of a set of species names✨
bp_taxonomy2tree(1p)Building a taxonomic tree based on the full lineages of a set of species names✨
bp_translate_seq(1)translates a sequence✨
bp_translate_seq(1p)translates a sequence✨
bp_tree2pag(1)convert Bio::TreeIO parseable format trees to pagel format✨
bp_tree2pag(1p)convert Bio::TreeIO parseable format trees to pagel format✨
bp_unflatten_seq(1)unflatten a genbank or genbank-style feature file into a nested SeqFeature hierarchy✨
bp_unflatten_seq(1p)unflatten a genbank or genbank-style feature file into a nested SeqFeature hierarchy✨
bpadmin(1)ION Bundle Protocol (BP) administration interface✨
bpcancel(1)Bundle Protocol (BP) bundle cancellation utility✨
bpchat(1)Bundle Protocol chat test program✨
bpclock(1)Bundle Protocol (BP) daemon task for managing scheduled events✨
bpcmp(1)compare ADIOS2 data files✨
bpcounter(1)Bundle Protocol reception test program✨
bpcp(1)A remote copy utility for delay tolerant networks utilizing NASA JPL's Interplanetary Overlay Network (ION)✨
bpcpd(1)ION Delay Tolerant Networking remote file copy daemon✨
bpdriver(1)Bundle Protocol transmission test program✨
bpecho(1)Bundle Protocol reception test program✨
bperp(1)bperp✨
bpf-addr2line(1)convert addresses or symbol+offset into file names and line numbers✨
bpf-ar(1)create, modify, and extract from archives✨
bpf-as(1)the portable GNU assembler.✨
bpf-c++filt(1)demangle C++ and Java symbols✨
bpf-dlltool(1)create files needed to build and use DLLs✨
bpf-elfedit(1)update ELF header and program property of ELF files✨
bpf-gdb(1)The GNU Debugger✨
bpf-gdb-add-index(1)Add index files to speed up GDB✨
bpf-gprof(1)display call graph profile data✨
bpf-gstack(1)Print a stack trace of a running program✨
bpf-ld(1)The GNU linker✨
bpf-ld.bfd(1)The GNU linker✨
bpf-nm(1)list symbols from object files✨
bpf-objcopy(1)copy and translate object files✨
bpf-objdump(1)display information from object files✨
bpf-ranlib(1)generate an index to an archive✨
bpf-readelf(1)display information about ELF files✨
bpf-size(1)list section sizes and total size of binary files✨
bpf-strings(1)print the sequences of printable characters in files✨
bpf-strip(1)discard symbols and other data from object files✨
bpf-unknown-none-lto-dump(1)Tool for dumping LTO object files✨
bpf-windmc(1)generates Windows message resources✨
bpf-windres(1)manipulate Windows resources✨
bping(1)Send and receive Bundle Protocol echo bundles.✨