diff options
| author | ben <ben@pkgsrc.org> | 2004-08-16 23:34:58 +0000 |
|---|---|---|
| committer | ben <ben@pkgsrc.org> | 2004-08-16 23:34:58 +0000 |
| commit | 7bf8866f8cc321bc596a41673ca0139041928492 (patch) | |
| tree | 09a38cfb5a0f5207168afe4065f1f1323c428330 /biology | |
| parent | ea4fc3dade3fb261b546c4394cc4e255e32f2c87 (diff) | |
| download | pkgsrc-7bf8866f8cc321bc596a41673ca0139041928492.tar.gz | |
Update to clustalw 1.83. Changes since 1.8 include:
* The FASTA format has been added to the list of alignment output
options.
* It is now possible to save the residue ranges (appended after the
sequence names) when saving a specified range of the alignment.
* The efficiency of the neighour-joining algorithm has been improved.
This work was done by Tadashi Koike at the Center for Information
Biology and DNA Data Bank of Japan and FUJITSU Limited.
Some example speedups are given below : (timings on a SPARC64 CPU)
No. of sequences original NJ new NJ
200 0' 12" 0.1"
500 9' 19" 1.4"
1000 XXXX 0' 31"
* ClustalW now returns error codes for some common errors when exiting.
This may be useful for people who run clustalw automatically from within
a script.
Error codes are:
1 bad command line option
2 cannot open sequence file
3 wrong format in sequence file
4 sequence file contains only 1 sequence (for multiple
alignments)
* Alignments can now be saved in Nexus format, for compatibility with
PAUP, MacClade etc. For a description of the Nexus format, see:
Maddison, D. R., D. L. Swofford and W. P. Maddison. 1997.
NEXUS: an extensible file format for systematic information.
Systematic Biology 46:590-621.
* Phylogenetic trees can also be saved in nexus format.
* A ClustalW icon has been designed for MAC and PC systems.
Diffstat (limited to 'biology')
| -rw-r--r-- | biology/clustalw/MESSAGE | 4 | ||||
| -rw-r--r-- | biology/clustalw/Makefile | 8 | ||||
| -rw-r--r-- | biology/clustalw/distinfo | 6 |
3 files changed, 9 insertions, 9 deletions
diff --git a/biology/clustalw/MESSAGE b/biology/clustalw/MESSAGE index f16843de438..77eb1381117 100644 --- a/biology/clustalw/MESSAGE +++ b/biology/clustalw/MESSAGE @@ -1,5 +1,5 @@ =========================================================================== -$NetBSD: MESSAGE,v 1.2 2002/09/12 17:08:22 wiz Exp $ +$NetBSD: MESSAGE,v 1.3 2004/08/16 23:34:58 ben Exp $ POLICY ON COMMERCIAL DISTRIBUTION OF CLUSTAL W @@ -8,7 +8,7 @@ W is increasingly being distributed as part of commercial sequence analysis packages. To help us safeguard future maintenance and development, commercial distributors of Clustal W must take out a NON-EXCLUSIVE LICENCE. Anyone wishing to commercially distribute -version 1.8 of Clustal W should contact the authors unless they have +version 1.83 of Clustal W should contact the authors unless they have previously taken out a licence. gibson@embl-heidelberg.de diff --git a/biology/clustalw/Makefile b/biology/clustalw/Makefile index a95d39b8c0c..478f68564b0 100644 --- a/biology/clustalw/Makefile +++ b/biology/clustalw/Makefile @@ -1,7 +1,7 @@ -# $NetBSD: Makefile,v 1.4 2004/01/29 13:34:24 grant Exp $ +# $NetBSD: Makefile,v 1.5 2004/08/16 23:34:58 ben Exp $ -DISTNAME= clustalw1.8.UNIX -PKGNAME= clustalw-1.8 +DISTNAME= clustalw1.83.UNIX +PKGNAME= clustalw-1.83 CATEGORIES= biology MASTER_SITES= ftp://ftp-igbmc.u-strasbg.fr/pub/ClustalW/ \ ftp://ftp.ebi.ac.uk/pub/software/unix/clustalw/ @@ -12,7 +12,7 @@ COMMENT= General purpose multiple alignment program for DNA or proteins MAKEFILE= makefile ALL_TARGET= clustalw -WRKSRC= ${WRKDIR}/clustalw1.8 +WRKSRC= ${WRKDIR}/clustalw1.83 MAKE_FLAGS+= CC="${CC}" diff --git a/biology/clustalw/distinfo b/biology/clustalw/distinfo index 38a692df2af..b2a53eb3a61 100644 --- a/biology/clustalw/distinfo +++ b/biology/clustalw/distinfo @@ -1,6 +1,6 @@ -$NetBSD: distinfo,v 1.2 2001/04/19 16:12:32 agc Exp $ +$NetBSD: distinfo,v 1.3 2004/08/16 23:34:58 ben Exp $ -SHA1 (clustalw1.8.UNIX.tar.gz) = 0765e056dffca93e08cba90bde89b69e69939e8d -Size (clustalw1.8.UNIX.tar.gz) = 4725425 bytes +SHA1 (clustalw1.83.UNIX.tar.gz) = 801ce911749171471b7964a1cff93c53c876c282 +Size (clustalw1.83.UNIX.tar.gz) = 166863 bytes SHA1 (patch-aa) = 96f95acb4a312c96440275ca65f7f908c9b9032f SHA1 (patch-ab) = 75fb21b88132bdf18e7f6bc13d1d35051a1babea |