[pkgsrc/trunk]: pkgsrc/biology/clustalw Update to clustalw 1.83. Changes sin...

[ben <ben%pkgsrc.org@localhost>]

details:   https://anonhg.NetBSD.org/pkgsrc/rev/f116339f6c81
branches:  trunk
changeset: 479555:f116339f6c81
user:      ben <ben%pkgsrc.org@localhost>
date:      Mon Aug 16 23:34:58 2004 +0000

description:
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:

 biology/clustalw/MESSAGE  |  4 ++--
 biology/clustalw/Makefile |  8 ++++----
 biology/clustalw/distinfo |  6 +++---
 3 files changed, 9 insertions(+), 9 deletions(-)

diffs (55 lines):

diff -r f83e4bb83d11 -r f116339f6c81 biology/clustalw/MESSAGE
--- a/biology/clustalw/MESSAGE  Mon Aug 16 23:32:04 2004 +0000
+++ b/biology/clustalw/MESSAGE  Mon Aug 16 23:34:58 2004 +0000
@@ -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 @@
 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@localhost
diff -r f83e4bb83d11 -r f116339f6c81 biology/clustalw/Makefile
--- a/biology/clustalw/Makefile Mon Aug 16 23:32:04 2004 +0000
+++ b/biology/clustalw/Makefile Mon Aug 16 23:34:58 2004 +0000
@@ -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 @@
 
 MAKEFILE=      makefile
 ALL_TARGET=    clustalw
-WRKSRC=                ${WRKDIR}/clustalw1.8
+WRKSRC=                ${WRKDIR}/clustalw1.83
 
 MAKE_FLAGS+=   CC="${CC}"
 
diff -r f83e4bb83d11 -r f116339f6c81 biology/clustalw/distinfo
--- a/biology/clustalw/distinfo Mon Aug 16 23:32:04 2004 +0000
+++ b/biology/clustalw/distinfo Mon Aug 16 23:34:58 2004 +0000
@@ -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