|
| EMBOSS-GCG comparison |
|
GCG Program |
EMBOSS or Other Alternative |
Third-party Package Needed | |
|---|---|---|---|
|
Direct Alternative |
Partial Alternative |
||
|
ASSEMBLE |
|||
|
BACKTRANSLATE |
|||
|
BESTFIT |
|||
|
BLAST |
BLAST package |
||
|
BREAKUP |
|||
|
CHOPUP |
Not needed |
||
|
CODONFREQUENCY |
|||
|
CODONPREFERENCE |
syco, wobble | ||
|
COILSCAN |
pepcoil | ||
|
COMPARE |
dottup, dotmatcher | ||
| COMPOSITION | compseq, pepstats | ||
|
COMPRESSTEXT |
shell script |
||
|
COMPTABLE |
|||
|
CONSENSUS |
|||
|
CORRESPOND |
|||
|
CORRUPT |
|||
|
DATASET |
|||
|
DETAB |
shell tools |
||
|
DISTANCES |
PHYLIP package |
||
|
DIVERGE |
PHYLIP package |
||
|
DOTPLOT |
|||
|
EXTRACTPEPTIDE |
|||
|
FASTA |
FASTA package |
||
|
FASTX |
FASTA package |
||
|
FETCH |
|||
|
FIGURE |
|||
|
FINDPATTERNS |
|||
|
FINGERPRINT |
|||
|
FRAMEALIGN |
wise2 |
||
|
FRAMES |
|||
|
FRAMESEARCH |
wise2 |
||
|
FROM* |
|||
|
GAP |
|||
|
GAPSHOW |
|||
|
GCGTOBLAST |
seqret / BLAST package |
||
|
GEL* |
Staden |
MSE |
|
|
GETSEQ |
|||
|
GROWTREE |
PHYLIP package, clustalw |
||
|
HELICALWHEEL |
|||
|
HTHSCAN |
|||
|
ISOELECTRIC |
|||
|
LINEUP |
mse |
||
|
LISTFILE |
gnu utils |
||
|
LOOKUP |
srs |
SRS | |
|
LPRINT |
gnu utils |
||
|
MAP |
|||
|
MAPPLOT |
|||
|
MAPSORT |
restrict |
||
|
MEME |
meme, pratt |
||
|
MFOLD |
mfold |
||
|
MOMENT |
|||
|
MOTIFS |
|||
|
MOTIFSEARCH |
|||
|
NAME |
Not required | setenv |
|
|
NAMES |
|||
|
NETBLAST |
BLAST package: blastcl3 |
||
|
NETFETCH |
|||
|
NOOVERLAP |
|||
|
OLDDISTANCES |
clustalw / PHYLIP package |
||
|
ONECASE |
shell |
||
|
OVERLAP |
|||
|
PAUPDISPLAY |
PAUP package |
||
|
PAUPSEARCH |
PAUP package |
||
|
PEPDATA |
shell and emboss |
||
|
PEPPLOT |
|||
|
PEPTIDEMAP |
|||
|
PEPTIDESORT |
|||
|
PILEUP |
clustalw |
||
|
PLASMIDMAP |
|||
|
PLOTFOLD |
|||
|
PLOTSIMILARITY |
|||
|
PLOTSTRUCTURE |
|||
|
PLOTTEST |
Not needed |
||
|
PRETTY |
|||
|
PRETTYBOX |
|||
|
PRIME |
|||
|
PROFILEGAP |
clustalw, prophet |
||
|
PROFILEMAKE |
|||
|
PROFILESCAN |
|||
|
PROFILESEARCH |
|||
|
PROFILESEGMENTS |
|||
|
PUBLISH |
|||
|
RED |
tex |
||
|
REFORMAT |
|||
|
REPEAT |
|||
|
REPLACE |
sed |
||
|
REVERSE |
|||
|
SAMPLE |
|||
|
SEG |
|||
|
SEGMENTS |
|||
|
SEQED |
mse |
||
|
SEQLAB |
|
EMBOSS.kaptn+KDE2, Apache+EMBOSS-GUI,
Jemboss+JDK+Java_WebStart,
| |
|
SETKEYS |
|||
|
SHIFTOVER |
|||
|
SHUFFLE |
|||
|
SIMPLIFY |
|||
|
SPEW |
linux |
||
|
SPSCAN |
|||
|
SSEARCH |
FASTA package |
||
|
STATPLOT |
gnuplot |
||
|
STEMLOOP |
|||
|
STRINGSEARCH |
textsearch, srs |
SRS | |
|
SYMBOL |
|||
|
TERMINATOR |
|||
|
TESTCODE |
|||
|
TFASTA |
FASTA package |
||
|
TFASTX |
FASTA package |
||
|
TO* |
|||
|
TRANSLATE |
|||
|
WINDOW |
|||
|
WORDSEARCH |
|||
|
XNU |
seg, xnu |
||