wrappers4EMBOSS 2.1.0

wrappers4EMBOSS allows to integrate under EMBOSS a number of popular bioinformatics software suites and databanks.
wrappers4EMBOSS allows to integrate under EMBOSS a number of popular bioinformatics software suites and databanks like BLAST, fastA, CLUSTAL, MUSCLE, CODEHOP, PROSITE, InterPro and some selected EBI Web Services, as well as to use MRS as EMBOSS sequence

wrappers4EMBOSS is included in the wEMBOSS release and is also distributed as a stand-alone package for people that run EMBOSS at the command line.

What's New in This Release:

· The installation script has been adapted so that it can work with EMBOSS 6.0.0 and MYEMBOSS 6.0.0. The current version of wrappers4EMBOSS hence should work rather well with all EMBOSS versions from 3.0.0 to 6.0.0.
· For wrappers that can open the output with a graphical viewer under X-Window the installation script asks whether you want to use this feature and will only check for the presence of these viewers if you say yes. This saves you the effort to install software you do not need.
· A new module ML (Maximum Likelihood) offers an interface to the programs PhyML of Stephane Guindon and Olivier Gascuel and ModelGenerator of Thomas Keane. The modelgenerator wrapper can optionally automatically launch PhyML on the selected best model. Both wrappers can when run in an X-terminal automatically open the generated tree file with NJplot.
· The module MRS supports now as well a local installation of MRS as a remote MRS server, which will be accessed though Web Services.
· The module EBI Web services has been upgraded with the latest version of the EBI Web Service clients, which function with the latest version of SOAP::Lite, so that there is no need anymore to support an installation of SOAP::Lite 0.60.
· The lists of databases in the menu's of ebi_blast and ebi_fasta from the module EBI Web services have been upgraded to the situation at the EBI server on 30 June 2008.
· The module fastA has been adapted to work with versions from 35.1.6 up to 35.3.6. In the list of program choices offered by fastasearch the defunct program tfasta has been removed and the new programs ggsearch and glsearch have been added ; the menu with amino acid matrices has been expanded too. For backward compatibility fastasearch and fastapid files adapted to versions 34.26.4 and 34.26.5 are still available.
· blast has an extra selector that allows the user to ask for composition based adjustment of the E() computation for the blastp and tblastn options (as is performed by default by psiblast and phiblast). Also, the on-line manuals for the BLAST module now contain information about allowed match/mismatch score + gap penalty combinations for nucleic acids.
· When run in an X-terminal clustalnj proposes to open an ordinary tree file with NJplot unrooted and a tree file with bootstrap values with NJplot rooted.
· If pf_make is run without UNIX shell it outputs a warning message "Note that if you are working under wEMBOSS the file does not show up in the output page but it is in your project.".
· In all the on-line manuals *.html the "Command line arguments" and the "See also" sections have been upgraded to the EMBOSS 4.0.0/5.0.0 format.

last updated on:
July 24th, 2008, 10:32 GMT
license type:
GPL (GNU General Public License) 
developed by:
Guy Bottu and Martin Sarachu
ROOT \ Science and Engineering \ Bioinformatics
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