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
_______________________________________________
EMBOSS mailing list
[email protected]
http://lists.open-bio.org/mailman/listinfo/emboss
