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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asnval
validate ASN.1 biological sequence records
asp-state
XSP - Mono ASP.NET Session State Server
asp-state4
XSP - Mono ASP.NET Session State Server
aspcud
solve dependencies between packages  
aspell-import
import old personal dictionaries into GNU Aspell
aspell
interactive spell checker
aspic
a line-art processor
aspline
Akima spline interpolation  
ass
autonomous system scanner
assa-genesis-3.5
assa-genesis - generates skeleton files for RAD development with ASSA library
assa-hexdump-3.5
assa-hexdump - Dump the contents of the file in hex to standard output
assembly-stats
get assembly statistics from FASTA and FASTQ files
assign_lisa
sgbdemos - Examples of the use of The Stanford GraphBase
assimp
Open Asset Import Library Tool
assword
impass - Simple and secure password management and retrieval system
astarithmetic
Arithmetic - arithmetic operations on images and numbers
astbuildprog
BuildProgram - compile, link with Gnuastro library and its dependencies, and run a C program
astcenc
compress or decompress images using the ASTC format
astconvertt
ConvertType - convert known data types to each other
astconvolve
Convolve - convolve an image with a given kernel
astcosmiccal
CosmicCalculator - estimate cosmological values
astcrop
Crop - crop regions of a dataset
astfits
Fits - view and manipulate FITS headers
astmatch
Match - match catalogs by 1D or 2D positions
astmkcatalog
MakeCatalog - Make a catalog from labeled input images
astmknoise
MakeNoise - add noise to an image
astmkprof
MakeProfiles - make standard 2D profiles on an image
astnoisechisel
NoiseChisel - detect signal in a noisy image
astquery
query - query remote data servers and download
astroid
graphical threads-with-tags style, lightweight and fast, e-mail client for Notmuch
astrometry-engine
Identify where a list of stars is on the sky
astscript-ds9-region
Create an SAO DS9 region file from a table
astscript-fits-view
View FITS images in DS9 and tables in TOPCAT based on contents
astscript-psf-scale-factor
Find factor to scale PSF to a given star in an image
astscript-psf-select-stars
Select good stars for constructing the PSF
astscript-psf-stamp
Make normalized stamp of star with background objects masked
astscript-psf-subtract
Subtract a given PSF model from the image of star
astscript-psf-unite
Unite the outer and inner regions of the PSF into one
astscript-radial-profile
Create a radial profile of an object in an image
astscript-sort-by-night
Sort input FITS files by night
astsegment
Segment - segmentation based on signal structure
aststatistics
Statistics - calculate statistics of a dataset
asttable
Table - read and write ASCII and FITS tables
astwarp
Warp - warp (transform) input dataset
astyle
multi-language indentation and reformatting filters  
asunder
graphical audio CD ripper and encoder  
asxxxx
ASxxxx - Series of microprocessor cross assemblers for SDCC
asy
Asymptote: a script-based vector graphics language
at
at, batch, atq, atrm - queue, examine, or delete jobs for later execution
at
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
atac
comparative mapping between genome sequences
ataglist
print audio file metadata
ataqv
QC metrics for ATAC-seq data
atari-convert-dir
helper for creating Atari compatible disk images
atari-hd-image
tool for creating a harddisk image for use with Hatari
atari800
emulator of Atari 8-bit computers and the 5200 console  
atari800.curses
atari800 - emulator of Atari 8-bit computers and the 5200 console  
atari800.sdl
atari800 - emulator of Atari 8-bit computers and the 5200 console  
atari800.x11
atari800 - emulator of Atari 8-bit computers and the 5200 console  
atdcat
syntax check and transformations of ATD files
atdgen
ATD compiler and code generator
atemswitch
CLI client for the OpenSwitcher proxy HTTP api
atest
Decode AX.25 frames from an audio file.  
atf-check
executes a command and analyzes its results
atf-sh
atf-sh [ -s
atf-test-program
common interface to ATF test programs
atfsit
A program to prepare files for version control
atfsrepair
repair corrupted AtFS repository, or convert old repository to new format
atftp
TFTP client (RFC1350)
athena-jot
jot - print sequential or random data
athena
interactive XAS data processing
aticonfig
parse an existing X-Server configuration file and modify it to operate with ATI products
atig
Another Twitter IRC Gateway
atigetsysteminfo
generate a system configuration report
atiodcli
System tray support for the ATI RADEON and FireGL control center
atiode
proprietary ATI RADEON and FireGL stress testing
atktopbm
convert Andrew Toolkit raster object to PBM  
atlc
an Arbitrary Transmission Line Calculator
atobm
bitmap, bmtoa, atobm - bitmap editor and converter utilities for the X Window System
atoms
make lists of atomic coordinates from crystallographic data
atoms
Atoms - Make lists of atomic coordinates from crystallographic data
atool
A script for managing file archives of various types
atop
Advanced System & Process Monitor
atopcat
concatenate raw log files to stdout
atopconvert
convert raw log file to newer version
atopsar
Advanced System Activity Report (atop related)
atq
at, batch, atq, atrm - queue, examine, or delete jobs for later execution
atril-previewer
show print preview for a document
atril-thumbnailer
create png thumbnails from atril supported documents
atril
Atril - The MATE Document Viewer
atrm
at, batch, atq, atrm - queue, examine, or delete jobs for later execution
atropos
NGS read trimming tool that is specific, sensitive, and speedy
atsc_epg
an electronic program guide using ATSC devices
atst-int32
atst - test the consistency of target architectures
atst-int64
atst - test the consistency of target architectures
atst-long
atst - test the consistency of target architectures
atst
test the consistency of target architectures
attachMesh
part of OpenFOAM (The Open Source CFD Toolbox)
attachtty
detachtty, attachtty - run an interactive program with io to a unix-domain socket
attr
extended attributes on filesystem objects