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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airspy_rx
probe device and show configuration
airspy_si5351c
chip register read/write tool
airspy_spiflash
program Flash
airspyhf_calibrate
show and set ppb calibration value
airspyhf_gpio
read and write gpio pin values
airspyhf_info
probe device and show configuration
airspyhf_lib_version
display AirSpyHF lib version
airspyhf_rx
probe device and show configuration
aj-snapshot
store and restore snapshots of JACK and/or ALSA connections
aj
aj, aj5 — command-line launchers for load-time weaving
aj5
aj, aj5 — command-line launchers for load-time weaving
ajbad
Test file for ACD parsing
ajbrowser
GUI to compile programs with ajc and navigate crosscutting structure
ajc
compiler and bytecode weaver for the AspectJ and Java languages
ajdoc
generate HTML API documentation, including crosscutting structure  
ajfeatest
Reads and writes (returns) a sequence and its features
ajlatex
latex command with japanese support of ASCII version
ajtest
Test file for ACD parsing
ajtex
tex command with japanese support of ASCII version
akaidump
Dump an AKAI media (i.e. CDROM) as disk image file to your HD
akaiextract
Extract audio samples from an AKAI media or AKAI disk image file
aklog-kafs
AFS Kerberos authentication tool
aklog
Obtain tokens for authentication to AFS
akonadictl
Akonadi server manipulation tool
al
al, al2 - Mono Assembly Linker
al2
al, al2 - Mono Assembly Linker
alacarte
Edit freedesktop.org menus
alacritty-msg
Send messages to Alacritty
alacritty
Alacritty - A fast, cross-platform, OpenGL terminal emulator
aladin
interactive software sky atlas
alarm-clock-applet
Alarm Clock for your notification area
albatross
a tool for finding fonts that contain a given (Unicode) glyph
album
Make a web photo album
alc
aLinkCreator - the aMule eD2k link creator
alcc
text based eD2k links calculator for aMule
aldo
A fully console morse code trainer written in ISO C++.  
ale-bin
ale - a synthetic capture engine and renderer
ale
a synthetic capture engine and renderer
alembic
lightweight database migration tool for usage with the SQLAlchemy
aleph
extended Unicode TeX
alevt-cap
capture teletext windows
alevt-date
print out UTC date
alevt
a teletext browser for analogue and DVB channels
alevt
X11 Teletext browser  
alevtd
webserver for videotext pages
alex
the lexical analyser generator for Haskell  
alf
Alignment free sequence comparison
alfa
automated line fitting algorithm
alfilldb
Add/update information of music files in the AudioLink database
algobox
algorithmics introduction software
algotutor
an interactive program for observing the intermediate steps of algorithms
ali
list mail aliases
ali
list nmh mail aliases
ali2gff
Module to translate a MUMmer output files into gff formatted output
ali2mol
alias
This manual page is part of the POSIX Programmer's Manual. The Linux implementation of this interface may differ (consult the corresponding Linux manual page for details of Linux behavior), or the interface may not be implemented on Linux
alice
App::Alice - an Altogether Lovely Internet Chatting Experience
alien
Convert or install an alien binary package
alien_hunter
Interpolated Variable Order Motifs for identification of horizontally acquired DNA  
align-columns
align the columns of tab-delimited input
align2kog.pl
converts an alignment into a kog file
align_dna
spliced align genomic sequence with cDNA
align_image_stack
Align overlapping images for HDR or focus stack creation
aligncopy
Reads and writes alignments
aligncopypair
Reads and writes pairs from alignments
alignment-cat
Concatenate several alignments (with the same sequence names) end-to-end
alignment-chop-internal
Remove ancestral sequences from an alignment
alignment-consensus
Construct a consensus alignment to summarize an alignment sample
alignment-distances
Compute distances between alignments
alignment-draw
Draw an alignment to HTML, optionally coloring residues by AU
alignment-find
Find the last (or first) FASTA alignment in a file
alignment-gild
Annotate each residue in the alignment according to the probability that it should align to the hypothetical root character in its column
alignment-indices
Show the alignment in terms of the index of each character in its sequence
alignment-info
Show useful statistics about the alignment
alignment-max
Construct a posterior decoding alignment to summarize an alignment sample
alignment-thin
Remove sequences or columns from an alignment
alignment-translate
Translate a DNA/RNA alignment into amino acids
alignmentProjector
alignments-diff
Align two alignments for comparison
aliki-rt
Measurement tool for Impulse Responses
aliki
Measurement tool for Impulse Responses
alimask
calculate and add column mask to a multiple sequence alignment  
alioth
elvi - surfraw(1) search tools  
alistat
show statistics for a multiple alignment file
all-knowing-dns
Tiny DNS server for IPv6 Reverse DNS
all_dists
Given a tree in Newick (*.nh) format, report distances
allcm
force the most important Computer-Modern-fonts to be calculated
allec
force the most important ec-fonts to be calculated
allegro-config
script to get information about the installed version of Allegro
allegro-dev-tools
collection of useful tools for Allegro 4 developers
alleleCounter
NGS copy number algorithms
alljoyn-daemon
The AllJoyn Message Bus Daemon version: v15.09.00a
allneeded
force the calculation of all fonts now needed
allpairs_master
executes All-Pairs workflow in parallel on distributed systems  
allpairs_multicore
executes All-Pairs workflow in parallel on a multicore machine  
allversusall
Sequence similarity data from all-versus-all comparison
allvirtualenv
virtualenvwrapper - a set of wrappers to assist with manage your python virtualenvs   All of the commands below are to be used on the Terminal command line
almanah
small GTK+ diary application
aln2bed
aln2bed converts ALN files to a BED file
aln2wig
convert alignments to wig files