[EMBOSS] Notes about emma

[Aengus Stewart]

Hi,

Some queries about emma

emma -help -verbose

gives the following section

  "-outseq" related qualifiers
   -osformat2           string     Output seq format
   -osextension2        string     File name extension
   -osname2             string     Base file name
   -osdirectory2        string     Output directory
   -osdbname2           string     Database name to add
   -ossingle2           boolean    Separate file for each entry
   -oufo2               string     UFO features
   -offormat2           string     Features format
   -ofname2             string     Features file name
   -ofdirectory2        string     Output directory
  "-dendoutfile" related qualifiers
   -odirectory3         string     Output directory

Though at the command line

emma -osformat clustal

or

emma -osformat2 clustal

or
emma -osf clustal

seem to work just as well.

-osformat2 seems to be a red herring?

Slightly more worrying is the clustal format header which the above
commands put in the .aln file

CLUSTAL W(1.4) multiple sequence alignment

I have just trawled the system and the only clustalw on it is from 1.82
If I run it as clustalw I get the correct

CLUSTAL W (1.82) multiple sequence alignment


Cheers
Aengus