section 1 · User commands 💻

68502 pages · page 19 of 343

A (continued)

awww-daemon(1)✨
awww-img(1)✨
awww-kill(1)✨
awww-pause(1)✨
awww-query(1)✨
awww-restore(1)✨
axcall(1)make an AX.25, NET/ROM or Rose connection.✨
axe-demux(1)axe Documentation Axe is a read de-multiplexer, useful in situations where sequence reads contain the indexes that uniquely distinguish samples. Axe uses a rapid and accurate algorithm based on…✨
axel(1)light command line download accelerator✨
axfer(1)command-line sound recorder and player for sound devices and nodes supported by Linux sound subsystem (Advanced Linux Sound Architecture, also known as ALSA).✨
axfer-list(1)dump lists of available sound devices and nodes to transfer audio data frame.✨
axfer-transfer(1)transferrer of audio data frame for sound devices and nodes.✨
axgetlist(1)read the message list from the BBS✨
axgetmail(1)automatically download messages from the F6FBB BBS✨
axgetmsg(1)download selected messages from F6FBB BBS✨
axgetput(1)upload or download files via AX.25 / axspawn Linux login session.✨
axhtpasswd(1)Manage user files for basic authentication✨
axhttpd(1)Demo HTTP/HTTPS server for axTLS✨
axi-cache(1)query the Apt Xapian Index✨
axiom(1)A general purpose computer algebra system✨
axiom-test(1)run the Axiom regression testsuite✨
AXIOMsys(1)A general purpose computer algebra system✨
axis(1)AXIS LinuxCNC Graphical User Interface✨
axis-remote(1)AXIS Remote Interface✨
axlisten(1)monitor AX.25 traffic✨
axohelp(1)helper program for use of LaTeX package axodraw2 with pdflatex.✨
axohelp(1texmf-dist)helper program for use of LaTeX package axodraw2 with pdflatex.✨
ayatana-webmail(1)Webmail Integration into your Desktop✨
ayatana-webmail-clear(1)Webmail Integration into your Desktop✨
ayatana-webmail-reset(1)Webmail Integration into your Desktop✨
ayatana-webmail-settings(1)Webmail Integration into your Desktop✨
ayatana-webmail-url(1)Webmail Integration into your Desktop (URL launcher)✨
aylet(1)play Spectrum `.ay' music files✨
aylet-gtk(1)play Spectrum `.ay' music files✨
azap(1)a program to process channels.conf files.✨
azorius(1)federated link sharer✨
azorius-filters(1)custom filtering✨
azorius-intro(1)introduction to azorius documentation✨
azove2(1)Another Zero-One Vertex Enumeration tool✨
azure-cosmos(1)azure-cosmos 3.1.1✨
azure-datalake-store(1)azure-datalake-store Documentation A pure-python interface to the Azure Data-lake Storage system, providing pythonic file-system and file objects, seamless transition between Windows and POSIX remote…✨
azure-protected-secrets-tool(1)inspect Azure Confidential VM state and unprotect host-provisioned secrets✨
azurecosmosdbsdkforpython(1)Azure CosmosDB SDK for Python 1.0.6✨
azuremetadata(1)Query Microsoft Azure metadata server✨

B

B(1)screen editor with structural regular expressions✨
b(1)build system driver✨
b1ee(1)Bluetooth device testing tool over internet✨
b2(1)Command-line utility to build Boost-related C++ projects with Boost.Build✨
b2-1.78(1)Command-line utility to build Boost-related C++ projects with Boost.Build✨
b2ct(1)converts the bracket notation produced by RNAfold into an '.ct' file✨
b2m.xemacs21(1)This program converts a babyl mailbox to a standard unix mailbox.✨
b2sum(1)compute and check BLAKE2 message digest✨
b3270(1)IBM host access tool back end✨
b3sum(1)manual page for b3sum 1.8.7✨
b4(1)Work with code submissions in a public-inbox archive✨
b43-fwcutter(1)Utility for extracting Broadcom 43xx firmware✨
b5i2iso(1)convert a BlindWrite image file into standard ISO image file✨
b64decode(1)encode / decode a binary file✨
b64encode(1)encode / decode a binary file✨
b91dec(1)basE91 encode or decode FILE, or standard input, to standard output✨
b91enc(1)basE91 encode or decode FILE, or standard input, to standard output✨
babel-minify(1)ES6+ aware minifier based on the Babel toolchain✨
babeljs(1)The compiler for writing next generation JavaScript✨
babeljs-7(1)The compiler for writing next generation JavaScript✨
babeljs-7-node(1)CLI that works exactly the same as the Node.js CLI, with the added benefit of compiling with Babel presets and plugins before running it✨
babeljs-node(1)CLI that works exactly the same as the Node.js CLI, with the added benefit of compiling with Babel presets and plugins before running it✨
babeltrace(1)Babeltrace Trace Viewer and Converter✨
babeltrace-log(1)Babeltrace Log Converter✨
babeltrace2(1)Convert or process one or more traces, and more✨
babeltrace2-convert(1)Convert one or more traces to a given format✨
babeltrace2-help(1)Get help for a Babeltrace 2 plugin or component class✨
babeltrace2-list-plugins(1)List Babeltrace 2 plugins and their properties✨
babeltrace2-query(1)Query an object from a Babeltrace 2 component class✨
babeltrace2-run(1)Create a Babeltrace 2 trace processing graph and run it✨
baby(1fun)create new process from two parents✨
backblaze-b2(1)B2 Command Line Tool✨
backbone_global_to_local(1)part of mauveAligner package alignmentProjector - part of mauveAligner package backbone_global_to_local - part of mauveAligner package bbAnalyze - part of mauveAligner package createBackboneMFA -…✨
backdoor-factory(1)inject predefined or user-defined shellcode in binaries✨
background(1)launch a command in the background, then go on with the execution flow✨
backintime(1)Create and manage incremental backups using rsync✨
backintime-askpass(1)Helper tool for *Back In Time*✨
backintime-config(1)BackInTime configuration files.✨
backintime-qt(1)Graphical Frontend for Back In Time✨
backport-dsc(1)backport Debian source packages✨
backportpackage(1)helper to test package backports✨
backstep(1)Backstep is a program that draws icons for minimized windows on your desktop.✨
backtick(1)run a program and stores its output in an environment variable, then execute another program✨
backtranambig(1e)Back-translate a protein sequence to ambiguous nucleotide sequence✨
backtranseq(1e)Back-translate a protein sequence to a nucleotide sequence✨
backup-checkallused(1)check chiark-backup configuration✨
backup-driver(1)entry point for cron or inittab to start backups✨
backup-labeltape(1)display or change tape label✨
backup-loaded(1)tell the chiark-backup system what to do with a new tape✨
backup-takedown(1)Bring some system services down for backups✨
backup-whatsthis(1)read an id off a tape and display it✨
backupchecker(1)fully automated backup checker✨
backupninja(1)A lightweight, extensible meta-backup system "a silent flower blossom death strike to lost data."✨
backuptodo(1)Make a backup archive of the todo.txt task file✨
bacon(1)small RSpec clone✨
bacteria_tradis(1p)Perform full tradis analysis✨
bacula-tray-monitor(1)Bacula's 'System Tray' monitor✨
badness(1)A formatter, linter, and language server for LaTeX✨
badness-debug(1)Debug utilities for parser and formatter diagnostics, and test scaffolding✨
badness-format(1)Format LaTeX source✨
badness-init(1)Write a commented starter `badness.toml` to the current directory✨
badness-inverse-search(1)Answer a PDF viewer's inverse (backward) search✨
badness-lint(1)Lint LaTeX source, reporting parse diagnostics✨
badness-lsp(1)Run the language server over stdio✨
badness-parse(1)Parse LaTeX source and print its concrete syntax tree (CST)✨
badwolf(1)minimalist and privacy-oriented web browser based on WebKitGTK✨
BaitFilter(1)manual page for BaitFilter-v1.0.6✨
BaitFisher(1)manual page for Error: Parameter file "--version" could not be opened. I guess it does not exist.✨
baka-mplayer(1)A free and open source, cross-platform, libmpv based multimedia player.✨
bake.php(1)generates skeleton CakePHP applications✨
baketextures(1)manual page for baketextures 1.39.5✨
balboa(1)BAsic Little Book Of Answers✨
balboa-backend-console(1)Backend maintenance console for balboa✨
balboa-bench(1)Run a number of queries against given endpoint✨
balboa-help(1)Help about any command✨
balboa-makeman(1)Create man pages✨
balboa-mock(1)Mock backend✨
balboa-query(1)Obtain information from pDNS about IP ranges✨
balboa-rocksdb(1)RocksDB backend for balboa✨
balboa-serve(1)Run the balboa frontend✨
bali-phy(1)Bayesian Inference of Alignment and Phylogeny✨
bali-phy-pkg(1)Manage BAli-Phy packages✨
bali-subsample(1)Subsample lines in a file.✨
BalloonContents(1x)Afterstep BalloonContents✨
balls(1)preprocessor for space-filling models in Raster3D molecular graphics package✨
BALLView(1)A free molecular modeling and molecular graphics tool✨
ballview(1)A free molecular modeling and molecular graphics tool✨
balsa(1)the GNOME e-mail client.✨
balsa-ab(1)the GNOME e-mail client.✨
bam(1)fast and flexible build system✨
bam-read(1)Parse bam files after multi-mapping reads have been assigned and aggregate read mapping information by contig.✨
bam12auxmerge(1)merge two BAM files✨
bam12split(1)project rank pairs produced by bamcollate2 to single ranks per read✨
bam12strip(1)remove rank left by bam12split from read names✨
bam2bed(1)manual page for bam2bed 2.4.42+dfsg✨
bam2bed_gnuParallel(1)manual page for bam2bed_gnuParallel 2.4.42+dfsg✨
bam2bed_sge(1)manual page for bam2bed_sge 2.4.42+dfsg✨
bam2bed_slurm(1)manual page for bam2bed_slurm 2.4.42+dfsg✨
bam2hints(1)convert mRNA-to-genome alignments in BAM format into a hint file for AUGUSTUS✨
bam2starch(1)manual page for bam2starch 2.4.42+dfsg✨
bam2starch_gnuParallel(1)manual page for bam2starch_gnuParallel 2.4.42+dfsg✨
bam2starch_sge(1)manual page for bam2starch_sge 2.4.42+dfsg✨
bam2starch_slurm(1)manual page for bam2starch_slurm 2.4.42+dfsg✨
bam2wig(1)Convert bam files to wiggle files. Can be used to generate exonpart hints for AUGUSTUS.✨
bam_pipeline(1)BAM pipeline of PALEOMIX suite✨
bam_rmdup_collapsed(1)filter BAM file for PCR duplicates✨
bamadapterclip(1)remove the adapters marked by bamadapterfind✨
bamadapterfind(1)find adapter contamination in sequencing reads✨
bamalignfrac(1)compute fraction of aligned bases in alignment file✨
bamauxmerge(1)merge information in unmapped and mapped alignment files✨
bamauxmerge2(1)merge information in unmapped and mapped BAM files✨
bamauxsort(1)filter auxiliary tags from BAM file✨
bambisect(1)find reduced size BAM file on which a program fails✨
BambooTracker(1)YM2608 (OPNA) tracker✨
bamcat(1)concatenate BAM files✨
bamchecksort(1)check sort order of a BAM file✨
bamcleanheader.py(1)remove illegal and malformed fields from a BAM file's header✨
bamclipreinsert(1)reinsert query sequence fragments removed by bamadapterclip✨
bamclipXT(1)reinsert query sequence fragments removed by bamadapterclip✨
bamcollate2(1)collate reads in a SAM, BAM or CRAM file by name✨
bamconsensus(1)compute rough consensus sequence from alignments✨
bamdownsamplerandom(1)downsample a SAM, BAM or CRAM file✨
bamfeaturecount(1)evaluate alignments produce by an RNA-seq aligner✨
bamfillquery(1)fill query sequences into BAM files✨
bamfilteraux(1)filter auxiliary tags from BAM file✨
bamfilterflags(1)remove entries from BAM files matching a given set of flags✨
bamfilterheader(1)filter auxiliary tags from BAM file✨
bamfilterheader2(1)filter auxiliary tags from BAM file✨
bamfiltermc(1)remove MC aux fields for reads with unmapped mates✨
bamfilterrg(1)filter read groups from a BAM file✨
bamfilterrg.py(1)filter readgroup(s) from a BAM file✨
bamfixflags.py(1)filter readgroup(s) from a BAM file✨
bamfixmateinformation(1)fix mate pair information in BAM files✨
bamflagsplit(1)sort BAM files by coordinate or query name✨
bamg(1rheolef)bidimensional anisotropic mesh generator (rheolef-7.2)✨
bamg2geo(1rheolef)convert bamg mesh in geo format (rheolef-7.2)✨
bamgroupreads.py(1)Group BAM file by read IDs without sorting✨
bamheadrg.py(1)Inject readgroup info✨
bamindex(1)create index for BAM file✨
bamintervalcomment(1)sort BAM files by coordinate or query name✨
bamlibs.py(1)output comma delimited string of read group IDs for each library✨
bammarkduplicates(1)mark duplicate reads/alignments in BAM files✨
bammarkduplicates2(1)mark duplicate reads/alignments in BAM files✨
bammarkduplicatesopt(1)mark duplicate reads/alignments in BAM files✨
bammaskflags(1)remove flags from alignments✨
bammdnm(1)compute MD and NM fields✨
bammerge(1)merge BAM files✨
bamrank(1)insert the rank (line number) of each alignment as an auxiliary field for tag zz✨
bamranksort(1)sort BAM files by rank✨
bamrecalculatecigar(1)concatenate BAM files✨
bamrecompress(1)recompress BAM file✨
bamreset(1)reset BAM file to unaligned state✨
bamseqchksum(1)produce checksums for primary data in BAM files✨
bamsormadup(1)sort name collated SAM or BAM file by coordinate and mark duplicates or sort SAM or BAM file by query name✨
bamsort(1)sort BAM files by coordinate or query name✨
bamsplit(1)split BAM files✨