EMBnet Norway

EMBOSS Substitutes for GCG programs

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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