[EMBOSS] wrappers4EMBOSS 2.3.0 released

Guy Bottu gbottu at vub.ac.be
Tue Aug 25 16:06:44 UTC 2009

	Dear users of wrappers4EMBOSS,

This mail concerns you if you are using or intend to use wrappers4EMBOSS 
with one of the following : EMBOSS 6.1.0, MRS 4, PhyML 3, CLUSTAL 2, 
InterProScan 4.5, EBI fastA access through Web Services.

You might be interested to upgrade for one of the following reasons :
- We support all EMBOSS versions from 3.0.0 to 6.1.0 (it was necessary 
to take account of the fact that MYEMBOSS can use "source" as well as 
"src" as directory name and that EMBOSS 6.1.0 requests to have parameter 
names that are unique in the first 6 characters).
- We support MRS version 4 as well as version 3.
- We have abandoned support for PhyML version 2 in favour of version 3. 
The wrapper for ModelGenerator has been modified accordingly in order to 
automatically start PhyML with a model generated by ModelGenerator, 
using not anymore the script generated by ModelGenerator itself (it is 
for version 2) but instead a Perl script that parses the ModelGenerator 
output. The user can choose whether to use the model selected according 
to Akaike, modified Akaike or Bayesian information criterion.
- We support the new optional features introduced in CLUSTAL version 2 
(using UPGMA instead of NJ, not using sequence weights, improving the 
alignment by iterative re-alignment).
- The module for InterProScan works with version 4.5 and has HAMAP in 
its menu.
- The list of databank names in ebi_fasta has been adapted to the recent 
situation on the server.

	Guy Bottu,
	wEMBOSS development team

More information about the EMBOSS mailing list