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.
Page 2
- Banner
- the AfterStep Logo module
- Barcode_split
- simple tool to split sequencing summary report in per barcodes
- Base
- Base - essential AfterStep configuration options
- BaselineFilter
- topp - library for LC/MS data management and analysis - tools
- BasiliskII-jit
- BasiliskII - a 68k Macintosh emulator
- BasiliskII-nojit
- BasiliskII - a 68k Macintosh emulator
- BasketLosses
- Example of Modeling Losses Across Correlated Assets
- BermudanSwaption
- Example of using QuantLib
- Bevel
- Bevel - Afterstep Bevel
- Bonds
- Example of bond pricing
- BuildConsensus.py
- Builds a consensus sequence for each set of input sequences
- BuildTrees.py
- Repertoire clonal assignment toolkit (Python 3)
- C-Sibelia.py
- comparing two microbial genomes
- CA.pl
- friendlier interface for OpenSSL certificate programs
- CAI
- calculate codon adaptation index for a DNA sequence
- CAT
- tool for taxonomic classification of contigs and metagenome-assembled genomes (MAGs)
- CDS
- Example of Credit-Default Swap pricing
- CEGUISampleFramework-0.8
- Sample program for the CEGUI system.
- CMEncrypt
- Send Encrypted Payload
- CTDConverter
- Convert CTD files into Galaxy tool and CWL CommandLineTool files
- CVAIRS
- Example of Credit Value Adjustment for Interest Rate Swap
- CVInspector
- topp - library for LC/MS data management and analysis - tools
- Calculator
- gnustep-examples - various example GNUstep tools/applications
- CallableBonds
- Example of callable-bond pricing
- Camera
- downloads files from your digital camera
- Canonicalise
- Canonicalise, CanonicaliseLazy - ‘cat’ filters for XML documents
- CanonicaliseLazy
- Canonicalise, CanonicaliseLazy - ‘cat’ filters for XML documents
- CartConvert
- - convert geodetic coordinates to geocentric or local cartesian
- Catrack
- dazzdb - manage nucleotide sequencing read data for the Dazzler assembler
- Ceni
- Curses /etc/network/interfaces
- Cenon
- vector graphics software for GNUstep
- Charmap
- a character map
- Chess
- Chess for GNUstep ported from OPENSTEP
- ChimeraSlayer
- chimeraslayer - detects likely chimeras in PCR amplified DNA
- ChromHMM
- Learning and analysis chromatin states using a multivariate Hidden Markov Model
- ChromImpute
- Large-scale systematic epigenome imputation
- ClonalFrame
- inference of bacterial microevolution using multilocus sequence data
- ClonalFrameML
- Efficient Inference of Recombination in Whole Bacterial Genomes
- CloudCompare
- 3D point cloud and mesh processing software
- ClusterMassTraces
- topp - library for LC/MS data management and analysis - tools
- ClusterMassTracesByPrecursor
- topp - library for LC/MS data management and analysis - tools
- ClusterSets.py
- Cluster sequences by group
- Cn3D-3.0
- Cn3D - a 3-dimensional viewer for biological molecules
- CollapseSeq.py
- emoves duplicate sequences from FASTA/FASTQ files
- ColorScheme
- ColorScheme - defines color values for standard set of internal color names, to be used in other configuration files
- CometAdapter
- topp - library for LC/MS data management and analysis - tools
- CompNovo
- topp - library for LC/MS data management and analysis - tools
- CompNovoCID
- topp - library for LC/MS data management and analysis - tools
- ConicProj
- - perform conic projections
- ConsensusID
- topp - library for LC/MS data management and analysis - tools
- ConsensusMapNormalizer
- topp - library for LC/MS data management and analysis - tools
- ConvertDb.py
- Repertoire clonal assignment toolkit (Python 3)
- ConvertHeaders.py
- Converts sequence headers to the pRESTO format
- ConvertibleBonds
- Example of using QuantLib to value convertible bonds
- CreateDOMDocument
- xerces-c - xerces-c sample program
- CreateGermlines.py
- Repertoire clonal assignment toolkit (Python 3)
- CruxAdapter
- topp - library for LC/MS data management and analysis - tools
- CsoundQt-d-cs6
- csoundqt - GUI interface and IDE for the csound synthesis system
- CubicSDR
- Software Defined Radio Application
- CuraEngine
- slicing engine for Cura
- CurrencyConverter
- gnustep-examples - various example GNUstep tools/applications
- CuteSdr
- CuteSDR - a simple demodulation and spectrum display program
- Cynthiune
- music player for GNUstep
- DAM2fasta
- dazzdb - manage nucleotide sequencing read data for the Dazzler assembler
- DAScover
- dascrubber - alignment-based scrubbing pipeline for DNA sequencing reads
- DASedit
- dascrubber - alignment-based scrubbing pipeline for DNA sequencing reads
- DASmap
- dascrubber - alignment-based scrubbing pipeline for DNA sequencing reads
- DASpatch
- dascrubber - alignment-based scrubbing pipeline for DNA sequencing reads
- DASqv
- dascrubber - alignment-based scrubbing pipeline for DNA sequencing reads
- DASrealign
- dascrubber - alignment-based scrubbing pipeline for DNA sequencing reads
- DAStrim
- dascrubber - alignment-based scrubbing pipeline for DNA sequencing reads
- DB2ONE
- dazzdb - manage nucleotide sequencing read data for the Dazzler assembler
- DB2arrow
- dazzdb - manage nucleotide sequencing read data for the Dazzler assembler
- DB2fasta
- dazzdb - manage nucleotide sequencing read data for the Dazzler assembler
- DB2quiva
- dazzdb - manage nucleotide sequencing read data for the Dazzler assembler
- DBModeler
- graphical management of relational database elements in GNUstep
- DBcp
- dazzdb - manage nucleotide sequencing read data for the Dazzler assembler
- DBdust
- dazzdb - manage nucleotide sequencing read data for the Dazzler assembler
- DBmv
- dazzdb - manage nucleotide sequencing read data for the Dazzler assembler
- DBrm
- dazzdb - manage nucleotide sequencing read data for the Dazzler assembler
- DBshow
- dazzdb - manage nucleotide sequencing read data for the Dazzler assembler
- DBsplit
- dazzdb - manage nucleotide sequencing read data for the Dazzler assembler
- DBstats
- dazzdb - manage nucleotide sequencing read data for the Dazzler assembler
- DBtrim
- dazzdb - manage nucleotide sequencing read data for the Dazzler assembler
- DBwipe
- dazzdb - manage nucleotide sequencing read data for the Dazzler assembler
- DHT_bootstrap
- A simple DHT bootstrap node
- DOMCount
- xerces-c - xerces-c sample program
- DOMPrint
- xerces-c - xerces-c sample program
- DPMDyMFoam
- part of OpenFOAM (The Open Source CFD Toolbox)
- DPMFoam
- part of OpenFOAM (The Open Source CFD Toolbox)
- DRAWEXE
- OpenCASCADE test harness
- DRAWxtl55
- drawxtl - display crystal structures on ordinary computer hardware
- DSMIDIWiFi
- DSMI over WLAN server
- DTAExtractor
- topp - library for LC/MS data management and analysis - tools
- DatabaseFilter
- topp - library for LC/MS data management and analysis - tools
- DatabaseSuitability
- topp - library for LC/MS data management and analysis - tools
- DeMeanderize
- topp - library for LC/MS data management and analysis - tools
- Decharger
- topp - library for LC/MS data management and analysis - tools
- DecoyDatabase
- topp - library for LC/MS data management and analysis - tools
- DefineClones.py
- Repertoire clonal assignment toolkit (Python 3)