GCG Program	Direct Alternative	Partial Alternative
ASSEMBLE		pasteseq
BACKTRANSLATE	backtranseq
BESTFIT	water, matcher
BLAST	BLAST package
BREAKUP	splitter
CHOPUP	Not needed
CODONFREQUENCY	compseq, chips, cusp
CODONPREFERENCE	syco, wobble
COILSCAN	pepcoil
COMPARE	dottup, dotmatcher
COMPOSITION	compseq, pepstats
COMPRESSTEXT		shell script
COMPTABLE
CONSENSUS	prophecy
CORRESPOND	codcmp
CORRUPT	msbar
DATASET	dbiflat, dbiblast, dbigcg
DETAB		shell tools
DISTANCES	PHYLIP package
DIVERGE	PHYLIP package
DOTPLOT	dottup/dotmatcher
EXTRACTPEPTIDE	transeq
FASTA	FASTA package
FASTX	FASTA package
FETCH	seqret
FIGURE
FINDPATTERNS	fuzznuc, fuzzprot
FINGERPRINT
FRAMEALIGN	wise2
FRAMES	plotorf, showorf
FRAMESEARCH	wise2
FROM*	seqret, seqretall
GAP	needle
GAPSHOW	plotcon
GCGTOBLAST	seqretall/BLAST package
GEL*	Staden	MSE
GETSEQ	newseq
GROWTREE	PHYLIP package, clustal
HELICALWHEEL	pepwheel
HTHSCAN	helixturnhelix
ISOELECTRIC	iep
LINEUP	mse
LISTFILE	gnu utils
LOOKUP	srs
LPRINT	gnu utils
MAP	restrict ,remap
MAPPLOT
MAPSORT	restrict
MEME	pratt
MFOLD	mfold
MOMENT	pepnet, octanol
MOTIFS	patmatmotifs
MOTIFSEARCH	profit
NAME	Not required	setenv
NAMES	infoseq	showdb
NETBLAST	BLAST package
NETFETCH	seqret, seqretall
NOOVERLAP	diffseq
OLDDISTANCES	clustal/PHYLIP package
ONECASE		shell
OVERLAP	supermatcher
PAUPDISPLAY	paup package
PAUPSEARCH	paup package
PEPDATA	getorf	shell and emboss
PEPPLOT	pepinfo
PEPTIDEMAP	digest
PEPTIDESORT
PILEUP	clustal
PLASMIDMAP	lindna
PLOTFOLD
PLOTSIMILARITY	plotcon
PLOTSTRUCTURE	pepinfo
PLOTTEST	Not needed
PRETTY	cons,prettyplot
PRETTYBOX	prettyplot
PRIME	prima
PROFILEGAP	clustal, prophet
PROFILEMAKE	prophecy
PROFILESCAN	patmatdb
PROFILESEARCH	profit
PROFILESEGMENTS
PUBLISH	seqretshowseq
RED		tex
REFORMAT	seqret
REPEAT	equicktandem, etandem, einverted, palindrome
REPLACE	sed
REVERSE	revseq
SAMPLE	extractseq
SEG		maskseq
SEGMENTS		matcher
SEQED	mse
SEQLAB		disGUIse
SETKEYS
SHIFTOVER
SHUFFLE	shuffelseq
SIMPLIFY
SPEW		linux
SPSCAN	sigcleave
SSEARCH	FASTA package
STATPLOT	gnuplot
STEMLOOP	palindrome einverted
STRINGSEARCH	textsearch, srs
SYMBOL
TERMINATOR
TESTCODE	wobble
TFASTA	FASTA package
TFASTX	FASTA package
TO*	seqret, seqretall
TRANSLATE	transeq
WINDOW	freak
WORDSEARCH
XNU	xnu

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