Section 1 of the manual describes user commands and tools, for example, file manipulation tools, shells, compilers, web browsers, file and image viewers and editors, and so on.

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alsearch
Search the AudioLink database for music
alt_getopt
parse command options
altair
simulate an altair computer
altairz80
simulate an Altair Z80 computer
alter-sequence-alignment
genomic sequences ALignment Transformation EnviRonment
altermime
MIME encoded email pack alteration tool  
altosui
Rocket flight monitor
altree-add-S
Title..
altree-convert
Title..
altree
Association and Localisation tests using phylogenetic Trees
alttab
the task switcher
alurecdplay
example program for playing CD tracks with alure
alureplay
example program for playing sounds with alure
alurestream
example program for sound streaming with alure
am7xxx-modeswitch
change the operational mode of am7xxx based devices
am7xxx-play
play stuff on an am7xxx device (e.g. Acer C110, PicoPix 1020)
amap
Protein multiple alignment by sequence annealing
amavis-logwatch
An Amavisd-new log parser and analysis utility
amazon
elvi - surfraw(1) search tools  
ambdec
Ambisonic decoder for first and second order
ambdec_cli
ambdec - Ambisonic decoder for first and second order
amberc
an elegant HTML templating engine written in Go.  
ambiguous_words
generate sets of words Tesseract is likely to find ambiguous
ambix-deinterleave
AMBIsonics eXchange utility
ambix-info
AMBIsonics eXchange utility
ambix-interleave
AMBIsonics eXchange utility
ambix-jplay
AMBIsonics eXchange utility
ambix-jrecord
AMBIsonics eXchange utility
amd64-mingw32msvc-addr2line
addr2line - convert addresses into file names and line numbers
amd64-mingw32msvc-ar
ar - create, modify, and extract from archives
amd64-mingw32msvc-as
AS - the portable GNU assembler
amd64-mingw32msvc-c++filt
c++filt - Demangle C++ and Java symbols
amd64-mingw32msvc-dlltool
dlltool - Create files needed to build and use DLLs
amd64-mingw32msvc-gprof
gprof - display call graph profile data
amd64-mingw32msvc-ld
ld - The GNU linker
amd64-mingw32msvc-nlmconv
nlmconv - converts object code into an NLM
amd64-mingw32msvc-nm
nm - list symbols from object files
amd64-mingw32msvc-objcopy
objcopy - copy and translate object files
amd64-mingw32msvc-objdump
objdump - display information from object files
amd64-mingw32msvc-ranlib
ranlib - generate index to archive
amd64-mingw32msvc-readelf
readelf - Displays information about ELF files
amd64-mingw32msvc-size
size - list section sizes and total size
amd64-mingw32msvc-strings
strings - print the strings of printable characters in files
amd64-mingw32msvc-strip
strip - Discard symbols from object files
amd64-mingw32msvc-windmc
windmc - generates Windows message resources
amd64-mingw32msvc-windres
windres - manipulate Windows resources
amdcccle
a GUI to setup a users desktop
amdgpu_plugin
ament_index
query the ROS 2 ament resource index
amf-to-stl
AMF to STL converter
amfora
Fancy terminal browser for the Gemini protocol
amide
AMIDE's a Medical Image Data Examiner
amideco
Decompress flashfiles equipped with an AMI BIOS
amidi
read from and write to ALSA RawMIDI ports  
aminer
lightweight tool for log checking, log analysis
aminerremotecontrol
lightweight tool for log checking, log analysis
amino-acid-composition
report amino acid composition
amispammer
The way to know if your MX IPs are blacklisted
amiwm
Amiga Workbench-like X Window Manager
amixer
command-line mixer for ALSA soundcard driver
amk_ccc-int32
amk_ccc, amk_fft2, amk_hy, amk_m2, amk_p2 - create target architectures
amk_ccc-int64
amk_ccc, amk_fft2, amk_hy, amk_m2, amk_p2 - create target architectures
amk_ccc-long
amk_ccc, amk_fft2, amk_hy, amk_m2, amk_p2 - create target architectures
amk_ccc
amk_ccc, amk_fft2, amk_hy, amk_m2, amk_p2 - create target architectures
amk_fft2-int32
amk_fft2 - utility command for SCOTCH
amk_fft2-int64
amk_fft2 - utility command for SCOTCH
amk_fft2-long
amk_fft2 - utility command for SCOTCH
amk_fft2
utility command for SCOTCH
amk_grf-int32
amk_grf - create target architecture from source graph
amk_grf-int64
amk_grf - create target architecture from source graph
amk_grf-long
amk_grf - create target architecture from source graph
amk_grf
create target architecture from source graph
amk_hy-int32
amk_hy - utility command for SCOTCH
amk_hy-int64
amk_hy - utility command for SCOTCH
amk_hy-long
amk_hy - utility command for SCOTCH
amk_hy
utility command for SCOTCH
amk_m2-int32
amk_m2 - utility command for SCOTCH
amk_m2-int64
amk_m2 - utility command for SCOTCH
amk_m2-long
amk_m2 - utility command for SCOTCH
amk_m2
utility command for SCOTCH
amk_p2-int32
amk_p2 - utility command for SCOTCH
amk_p2-int64
amk_p2 - utility command for SCOTCH
amk_p2-long
amk_p2 - utility command for SCOTCH
amk_p2
utility command for SCOTCH
amo-changelog
fetch Version History of an addon
amoeba
Fast-paced, polished OpenGL demonstration by Excess  
amp2response
MRtrix3 - diffusion-weighted MRI white matter tractography
amp2sh
MRtrix3 - diffusion-weighted MRI white matter tractography
ampID
Echo Device Key  
ampboot
Qualcomm Atheros AR7x00 Powerline Device Bootstrapper  
ampctl
control radio amplifiers
ampctld
TCP amplifier control daemon
amphost
Qualcomm Atheros Powerline Device Host Emulator  
ample
Ample MP3 server
ampliconnoise
AmpliconNoise - remove noise from high throughput nucleotide sequence data
amplist
List Atheros Device Addresses  
amprate
Qualcomm Atheros AR7x00 PHY Rate Monitor  
amprule
Stream Classification Utility  
ampstat
Qualcomm Atheros AR7x00 Link Statistics  
amptest
Qualcomm Atheros PLC Test Applet Loader