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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aevol_misc_create_eps
Aevol - an in silico experimental evolution platform
aevol_misc_extract
Aevol - an in silico experimental evolution platform
aevol_misc_gene_families
aevol - an in silico experimental evolution platform
aevol_misc_lineage
Aevol - an in silico experimental evolution platform
aevol_misc_robustness
Aevol - an in silico experimental evolution platform
aevol_misc_view
Aevol - an in silico experimental evolution platform
aevol_modify
Aevol - an in silico experimental evolution platform
aevol_propagate
Aevol - an in silico experimental evolution platform
aevol_run
Aevol - an in silico experimental evolution platform
aewan
An ascii-art editor  
aewm++
a minimalistic window manager for X11
aewm++_appbar
a small application launcher
aewm++_fspanel
small panel
aewm++_setrootimage
puts a nice diagonal gradient image on the root window
aewm++_xsession
keeps an xsession alive
afdconnectivity
MRtrix3 - diffusion-weighted MRI white matter tractography
afdko
wrapper for afdko utilities
afetch
retrieve an alignment from an alignment database
afew
afex
client for anonymous FEX
affcat
Output contents of an image file to stdout
affcompare
compare the contents of an ISO file to an AFF file
affconvert
convert files between RAW and AFF formats
affcopy
reorder and recompress AFF files
affcrypto
handle encryption issues
affdiskprint
create a diskprint AFF structure
affinfo
print information about an AFF file
affix
fix a corrupted AFF file
affrecover
recover broken pages of an AFF file
affsegment
segment manipulation tool
affsign
sign an existing AFF file
affstats
print specific statistics about one or more AFF files
affuse
provide access to AFF containers
affverify
verify the digital signature on a signed file
affxml
print AFF information as XML
afio
manipulate archives and files
afm2afm
reencode an afm file
afm2pl
convert AFM font metrics to TeX pl font metrics
afm2tfm
convert Adobe font metrics to TeX font metrics
afmtodit
create font files for use with groff -Tps and -Tpdf
afnix-adp
afnix-us-adp - afnix documentation processor
afnix-axc
axc - afnix cross compiler
afnix-axd
axd - afnix cross debugger
afnix-axi
axi - afnix cross interpreter
afnix-axl
axl - afnix cross librarian
afnix-axp
afnix-us-axp - afnix xml processor
afs-up
up - Recursively copy directories, preserving AFS metadata
afs
Introduction to AFS commands
afs_compile_et
Produce error text tables for compilation
afslog
obtain AFS tokens
afsmonitor
Monitors File Servers and Cache Managers
afssh
wrapper around ssh-agent-filter and ssh
aft-mtp-cli
reliable MTP client with minimalistic UI
aft-mtp-mount
reliable MTP client with minimalistic UI
aft
"free form" document preparation system  
afterimage-config
script to get information about the installed version of libAfterImage
afterimage-libs
script to get information about the installed version of libAfterImage
afterstep
AfterStep  - X11 window manager  
afterstep_faq
afterstep_faq  - This document is an ever growing set of questions, statements, ideas and complaints about AfterStep version 2.0  
afterstepdoc
show AfterStep's documentation
afuse
AFUSE - automounting file system implemented in user-space using FUSE
ag++
a frontend to ac++ and g++
ag
The Silver Searcher. Like ack, but faster
age-keygen
generate age(1) key pairs
age
simple, modern, and secure file encryption
agedu
correlate disk usage with last-access times to identify large and disused data
agentxtrap
send an AgentX NotifyPDU to an AgentX master agent
aggregartp
Splits a single RTP stream to several contribution links with load balancing
aggregate-ios
optimise a concatenated set of cisco/IOS prefix filters to help make them nice and short.  
aggregate
optimise a list of route prefixes to help make nice short filters  
agh-profile-gen
- Sleep profile generator using various metrics
aghermann
Aghermann -- a sleep research experiment manager and Achermann et al (1993) model simulator
agmrancid
rancid - Cisco configuration filter
agreety
A text-based greeter for greetd
agrep
search a file for a string or regular expression, with approximate matching capabilities
agusload
load a GUS-format patch file into the AWE32 RAM
aha
Convert ANSI escape sequences to HTML
aid
Query ID database and report results
aide
Advanced Intrusion Detection Environment
aidl-cpp
C++ bindings generator of AIDL interfaces
aidl
Java bindings generator of AIDL interfaces
aiksaurus
Aiksaurus - English-language thesaurus
aimk
Portable make wrapper script
ainsl
AppendIfNoSuchLine
aiohttp-wsgi-serve
run a WSGI application
aiosmtpd
air-quality-sensor
User space driver for AppliedSensor's Indoor Air Monitor
aircrack-ng
a 802.11 WEP / WPA-PSK key cracker
airdecap-ng
decrypt a WEP/WPA crypted pcap file
airdecloak-ng
airuncloak-ng - Removes wep cloaked framed from a pcap file
airgraph-ng
a 802.11 visualization utility  
airodump-join
a support tool for airgraph-ng that allows you to join the airodump output files.  
airolib-ng
manage and create a WPA/WPA2 pre-computed hashes tables
airr-tools
Data Representation Standard library for antibody and TCR sequences
airscan-discover
Discover sane-airscan compatible scanners
airspy_gpio
read and write gpio pin values
airspy_gpiodir
reconfigure GPIO Direction
airspy_info
probe device and show configuration
airspy_lib_version
display AirSpy lib version
airspy_r820t
The Airspy is a tiny and efficient software defined radio receiver. This application lets the user probe the device and show configuration