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authorben <ben@pkgsrc.org>2004-08-16 23:34:58 +0000
committerben <ben@pkgsrc.org>2004-08-16 23:34:58 +0000
commit7bf8866f8cc321bc596a41673ca0139041928492 (patch)
tree09a38cfb5a0f5207168afe4065f1f1323c428330 /biology/clustalw/Makefile
parentea4fc3dade3fb261b546c4394cc4e255e32f2c87 (diff)
downloadpkgsrc-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/clustalw/Makefile')
-rw-r--r--biology/clustalw/Makefile8
1 files changed, 4 insertions, 4 deletions
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}"