The EMBASSY Packages

 

EMBASSY Packages

Contents

DOMAINATRIX

Previous dirstributions of the protein domain programs from Jon Ison's group were in a single EMBASSY package. This is now split into 5 packages according to function.

Application details and documentation for DOMAINATRIX

DOMAINATRIX is available as a Beta release 0.1.0 from our FTP server ftp://emboss.open-bio.org/pub/EMBOSS/ in file DOMAINATRIX-0.1.0.tar.gz

Application details and documentation for DOMALIGN

DOMALIGN is available as a Beta release 0.1.0 from our FTP server ftp://emboss.open-bio.org/pub/EMBOSS/ in file DOMALIGN-0.1.0.tar.gz

Application details and documentation for DOMSEARCH

DOMSEARCH is available as a Beta release 0.1.0 from our FTP server ftp://emboss.open-bio.org/pub/EMBOSS/ in file DOMSEARCH-0.1.0.tar.gz

Application details and documentation for SIGNATURE

SIGNATURE is available as a Beta release 0.1.0 from our FTP server ftp://emboss.open-bio.org/pub/EMBOSS/ in file SIGNATURE-0.1.0.tar.gz

Application details and documentation for STRUCTURE

STRUCTURE is available as a Beta release 0.1.0 from our FTP server ftp://emboss.open-bio.org/pub/EMBOSS/ in file STRUCTURE-0.1.0.tar.gz

EMNU (EMBOSS Menu is Not UNIX)

Application details and documentation for EMNU

EMNU is available as release 1.05 from our FTP server ftp://emboss.open-bio.org/pub/EMBOSS/ in file EMNU-1.05.tar.gz

This EMBASSY package is no longer maintained and is considered to be obsolete. There are many better EMBOSS interfaces avaialble. We plan to remove it from a future release.

ESIM4 (EMBOSS version of SIM4)

Application details and documentation for ESIM4

ESIM4 is available as release 1.0.0 from our FTP server ftp://emboss.open-bio.org/pub/EMBOSS/ in file ESIM4-1.0.0.tar.gz

HMMER (EMBOSS wrappers for HMMER 2.3.2)

Previous releases included an EMBASSY package HMMER which was a port of a release of the HMMER package. We were unable to find the time to update this release, and have changed our approach. The new port uses a simple wrapper approach which has some limitations but has more chance of being updated.

Application details and documentation for HMMERNEW

HMMER 2.3.2 are available from our FTP server ftp://emboss.open-bio.org/pub/EMBOSS/ in file HMMER-2.3.2.tar.gz

MEMENEW (EMBOSS wrappers for MEME)

Application details and documentation for MEMENEW

MEMENEW is available as release 0.1.0 from our FTP server ftp://emboss.open-bio.org/pub/EMBOSS/ in file MEME-0.1.0.tar.gz

MSE (A Multiple Sequence Screen Editor for Biological Sequences.)

Application details and documentation for MSE

MSE is available as release 1.0.0 from our FTP server ftp://emboss.open-bio.org/pub/EMBOSS/ in file MSE-1.0.0.tar.gz

MYEMBOSS (For sites to build their own applications)

Application details and documentation for MYEMBOSS

MYEMBOSS provides a directory structure and makefile stubs for developing your own applications more easily than in versions before 3.0.0.

MYEMBOSS requires autoconf, automake and libtool to be installed. See the INSTALL file for more informations.

MYEMBOSS is available as release 3.0.0 from our FTP server ftp://emboss.open-bio.org/pub/EMBOSS/ in file MYEMBOSS-3.0.0.tar.gz

PHYLIPNEW (Phylogeny Inference Package)

Application details and documentation for PHYLIP and PHYLIPNEW.

PHYLIP 3.572 was available as an EMBASSY package with previous releases. In 3.0.0 we included a beta test conversion of PHYLIP 3.61 (PHYLIPNEW) which is now a fully supported EMBASSY package. Program names now begin with 'f' rather than 'e' and interfaces are more EMBOSS-like. Please pass on feedback to our bug reporting list emboss-bug@emboss.open-bio.org

PHYLIPNEW is available from our FTP server ftp://emboss.open-bio.org/pub/EMBOSS/ in file PHYLIPNEW-3.6b.tar.gz

TOPO (Transmembrane display)

Application details and documentation for TOPO

TOPO is available as release 1.0.0 from our FTP server ftp://emboss.open-bio.org/pub/EMBOSS/ in file TOPO-1.0.0.tar.gz

VIENNA (RNA structure)

Application details and documentation for VIENNA

VIENNA is a port of release 1.6 of Ivo Hofacker's ViennaRNA package.

VIENNA is available as release 1.6 from our FTP server ftp://emboss.open-bio.org/pub/EMBOSS/ in file VIENNA-1.6.tar.gz