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Diffstat (limited to 'academic/EMBASSY/CONTENTS')
| -rw-r--r-- | academic/EMBASSY/CONTENTS | 122 |
1 files changed, 46 insertions, 76 deletions
diff --git a/academic/EMBASSY/CONTENTS b/academic/EMBASSY/CONTENTS index d739dcfb711e..bd0665b82b44 100644 --- a/academic/EMBASSY/CONTENTS +++ b/academic/EMBASSY/CONTENTS @@ -1,94 +1,64 @@ -The EMBASSY package includes the following: -------------------------------------------- +CBSTOOLS: The CBSTOOLS package is a set of wrappers to selected +applications from the CBS group in Denmark. -DOMAINATRIX Previous distributions 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. +CLUSTALOMEGA: A wrapper for the clustal omega application. -Application details and documentation for DOMAINATRIX +DOMAINATRIX: The DOMAINATRIX programs were developed by Jon Ison and +colleagues at MRC HGMP for their protein domain research. They are +included as an EMBASSY package as a work in progress. -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 +DOMALIGN: The DOMALIGN programs were developed by Jon Ison and +colleagues at MRC HGMP for their protein domain research. They are +included as an EMBASSY package as a work in progress. -Application details and documentation for DOMALIGN +DOMSEARCH: The DOMSEARCH programs were developed by Jon Ison and +colleagues at MRC HGMP for their protein domain research. They are +included as an EMBASSY package as a work in progress. -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 +EMNU: The EMNU package is a simple EMBOSS menu system written by Gary +Williams at HGMP. -Application details and documentation for DOMSEARCH +ESIM4: The ESIM4 package is an EMBOSS conversion of the SIM4 package +from Liliana Florea. -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 +HMMER: A suite of application wrappers to the original hmmer v2.3.2 +applications written by Sean Eddy. hmmer v2.3.2 must be installed on +the same system as EMBOSS and the location of the hmmer executables +must be defined in your path for EMBASSY HMMER to work. -Application details and documentation for SIGNATURE +IPRSCAN: The IPRSCAN package is a wrapper for the interproscan +program. -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 +MEME: The EMBASSY MEME package contains 'wrapper' applications +providing an EMBOSS-style interface to the applications in the +original MEME package version 4.0.0 developed by Timothy L. Bailey. -Application details and documentation for STRUCTURE +MIRA: The MIRA package is a fragment assembly program from Bastien +Chevreux. The program was converted to EMBOSS by Alan Bleasby as two +applications, one for EST assembly and one for shotgun fragment +assembly -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 +MSE: The MSE package is a multiple sequence editor. The program was +contributed to the EMBOSS package by the author, Will Gilbert, as one +of the first EMBASSY programs. -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 ESIM4 -(EMBOSS version of SIM4) Application details and documentation for ESIM4 +MYEMBOSS: A package for your own software developments. -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 version of HMMER 2.1.1 - PLEASE USE HMMERNEW) Application details -and documentation for HMMER +MYEMBOSSDEMO: The MYEMBOSSDEMO package contains example applications +using EMBOSS data types -HMMER is available as release 2.1.1 from our FTP server -ftp://emboss.open-bio.org/pub/EMBOSS/ in file HMMER-2.1.1.tar.gz HMMERNEW -(EMBOSS version of HMMER 2.3.2) Application details and documentation -for HMMERNEW +PHYLIPNEW: The PHYLIPNEW programs are EMBOSS conversions of the +programs in Joe Felsenstein's PHYLIP package, version 3.69. -HMMER 2.3.2 is available from our FTP server -ftp://emboss.open-bio.org/pub/EMBOSS/ in file HMMER-2.3.2.tar.gz -MEME (previous EMBOSS version of MEME 2.3.1) Application details and -documentation for MEME +SIGNATURE: The SIGNATURE programs were developed by Jon Ison and +colleagues at MRC HGMP for their protein domain research. They are +included as an EMBASSY package as a work in progress. -MEME is available as release 2.3.1 from our FTP server -ftp://emboss.open-bio.org/pub/EMBOSS/ in file MEME-2.3.1.tar.gz MEMENEW -(EMBOSS version of MEME 3.0.14) Application details and documentation -for MEMENEW which wraps release 3.0.14 of the Meme package +STRUCTURE: The STRUCTURE programs were developed by Jon Ison and +colleagues at MRC HGMP for their protein domain research. They are +included as an EMBASSY package as a work in progress. -MEMENEW is available as release 0.1.0 from our FTP server -ftp://emboss.open-bio.org/pub/EMBOSS/ in file MEMENEW-0.1.0.tar.gz -MSE (A Multiple Sequence Screen Editor for Biological Sequences.) -Application details and documentation for MSE +TOPO: The TOPO package is a graphics program to display membrane +protein topology by Susan Jean Johns. -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 1.0.0 from our FTP server -ftp://emboss.open-bio.org/pub/EMBOSS/ in file MYEMBOSS-1.0.0.tar.gz PHYLIP -(Phylogeny Inference Package) Application details and documentation for -PHYLIP and PHYLIPNEW. - -PHYLIP 3.572 was available as an EMBASSY package with previous -releases. From 3.0.0 we are including a beta test conversion of PHYLIP -3.61 (PHYLIPNEW). 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 as a Beta release 3.6b from our FTP server -ftp://emboss.open-bio.org/pub/EMBOSS/ in file PHYLIP-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 package Application details and documentation for VIENNA - -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 +VIENNA: These programs are adapted from the VIENNA RNA package. |