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