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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au
Network Audio System - a portable, network-transparent audio system
aubio
a command line tool to extract information from sound files
aubiocut
a command line tool to slice sound files at onset or beat timestamps
aubiomfcc
a command line tool to compute Mel-Frequency Cepstrum Coefficients
aubionotes
a command line tool to extract musical notes
aubioonset
a command line tool to extract musical onset times
aubiopitch
a command line tool to extract musical pitch
aubioquiet
a command line tool to extracts quiet and loud regions from a file
aubiotrack
a command line tool to extract musical beats from audio signals
aucat
audio files manipulation tool
auconvert
perform various conversion operations on sound files
auctl
control various audio server parameters
audacious
an advanced audio player.  
audacity
Graphical cross-platform audio editor
audemo
Network Audio System record and play demo
audial
generate or recognize touch tones for North American telephones
audio2tape
Sinclair ZX Spectrum audio to tape file converter
audio_rename
rename an audio file via information got via MP3::Tag
audiolink
Create AudioLink config file, databases and tables
audiotools-config
manage Python Audio Tools configuration
audit2allow
generate SELinux policy allow/dontaudit rules from logs of denied operations  
audit2why
audit2allow - generate SELinux policy allow/dontaudit rules from logs of denied operations  
audtool
a small tool to control Audacious from the command line.  
audtty
Control Audacious from the command line with a friendly ncurses interface
auedit
graphically record and edit audio files
augmatch
inspect and match contents of configuration files
augparse
execute an Augeas module
augprint
create an idempotent augtool script for a given file
augtool
inspect and modify configuration files
augur
pipeline components for real-time virus analysis
augustus
a gene prediction tool
auinfo
show information about a Network Audio System server
aumeta
move seek index and adjust metadata of audio files
aumix
adjust audio mixer
aunpack
atool - A script for managing file archives of various types
aupanel
allows user adjustment of Network Audio System device attributes
auphone
a simple telephone client
auplay
play a sound file to a Network Audio System server
aur
elvi - surfraw(1) search tools  
aurecord
record a sound file from a Network Audio System server
auscope
Network Audio System Protocol Filter
austin
manual page for austin 1.0.1
austlii
elvi - surfraw(1) search tools  
authbind
bind sockets to privileged ports without root
authoritydbus
Perform the settings that require the right to be raised
authorized-keys-test
Validate a authorized_keys file
authpasswd
Generate login passwords
authprogs
SSH command authenticator
authtest
Test the Courier Authentication Library
authvar
handles authenticated variables for pesign  
auto-07p
The AUTO command line user interface
auto-apt-proxy
autodetect common APT proxy setups
auto-multiple-choice-analyse
automatic data capture from scans for AMC multiple choice exams
auto-multiple-choice-annotate
completed answer sheets annotation after marking for AMC multiple choice exams
auto-multiple-choice-association-auto
automatic association between students and answer sheets for AMC multiple choice exams
auto-multiple-choice-association
manual association between students and answer sheets for AMC multiple choice exams
auto-multiple-choice-export
exports marks for AMC multiple choice exams
auto-multiple-choice-getimages
prepares scan images before sending them to auto-multiple-choice-analyse (1) for analysis
auto-multiple-choice-imprime
prints AMC multiple choice answer sheets to be distributed to the students
auto-multiple-choice-mailing
mail PDF annotated completed answer sheets to students
auto-multiple-choice-meptex
gets the layout information from the working document to the layout database
auto-multiple-choice-note
computes marks after scans data capture for AMC multiple choice exams
auto-multiple-choice-prepare
prepares working documents from LaTeX source file
auto-multiple-choice
Automated treatment of MCQs
autoPatch
part of OpenFOAM (The Open Source CFD Toolbox)
autobk
automatic XAFS background removal
autoclass
automatically discover classes in data
autoconf-dickey
autoconf - Generate configuration scripts
autoconf
Generate configuration scripts
autoconf2.13
creates scripts to configure source code packages using templates
autoconf2.64
autoconf - Generate configuration scripts
autoconf2.69
autoconf - Generate configuration scripts
autocutsel
keep the X clipboard and the cutbuffer in sync
autodep8
DEP-8 test control file generator
autodia
a perl script using the Autodia modules to create UML Class Diagrams or documents. from code or other data sources
autodock4
autodock - docking of chemical ligands to protein receptors
autodocktools
adt - AutoDockTools, a graphical front-end for AutoDock
autoexpect
generate an Expect script from watching a session
autoflake
removes unused imports and unused variables in Python code
autogen
The Automated Program Generator
autogrid4
autogrid - preparing protein and ligand for AutoDock analysis
autogsdoc
GNUstep API documentation generator and XML->HTML converter  
autoheader-dickey
autoheader - Create a template header for configure
autoheader
Create a template header for configure
autoheader2.13
creates a template file of C #define's for use by configure
autoheader2.64
autoheader - Create a template header for configure
autoheader2.69
autoheader - Create a template header for configure
autoimport
Automatically add import statements to Python code
autoinst
wrapper around the LCDF TypeTools, for installing and using OpenType fonts in LaTeX
autojump
a faster way to navigate your filesystem
autokey-gtk
keyboard automation utility for GNOME and GTK
autokey-qt
keyboard automation utility for KDE and QT
autokey-run
command-line execution utility for AutoKey
autoligand
AutoLigand: - identification of a receptor's ligand binding site
autom4te
Generate files and scripts thanks to M4
autom4te2.64
autom4te - Generate files and scripts thanks to M4
autom4te2.69
automake-1.11
automake - manual page for automake 1.11.6
automake-1.16
automake - manual page for automake 1.16.5
autool
audio play/record tool compatible with audiotool