Clustal W

Clustal W is a sequence alignment tool for nucleic acid sequences:

Overview

Modifications

Download information

Overview

The multiple sequence alignment tool Clustal W was developed by Julie Thompson and Toby Gibson (both at EMBL, Heidelberg, Germany) and Des Higgins (University of County Cork, Cork, Ireland). The tool uses sequence weighting, positions-specific gap penalties and weight matrix choice to improve the sensitivity of progressive multiple sequence alignment. A online paper describing the algorithms can be found at the Clustal W homepage.

The CygWin port is based on Clustal W version 1.8.

Modifications

The source code is ANSI C and compiles with gcc, so it took only minor modifications in the makefile to compile on WinNT.

makefile

The first part of the diff eliminates two tabs that GNU make complains about. The second part sets the c compiler to gcc.

--- /Temp/install-files/clustalw1.8/makefile	Thu Sep 11 07:03:16 1997
+++ makefile	Wed Jul 14 22:15:30 1999
@@ -4,13 +4,13 @@
 	rm *.o
 
 OBJECTS = interface.o sequence.o showpair.o malign.o \
-  	util.o trees.o gcgcheck.o prfalign.o pairalign.o \
-  	calcgapcoeff.o calcprf1.o calcprf2.o calctree.o \
-        readmat.o alnscore.o random.o 
+          util.o trees.o gcgcheck.o prfalign.o pairalign.o \
+          calcgapcoeff.o calcprf1.o calcprf2.o calctree.o \
+          readmat.o alnscore.o random.o 
 
 HEADERS = general.h clustalw.h
 
-CC	= cc
+CC	= gcc
 CFLAGS  = -c -O
 LFLAGS	= -O -lm

System requirements

I used the following setup to build the software:

Windows NT 4.0 SP3 Workstation
gcc-2.95
CygWinB20.1

With this setup, make gives a clean build.

To install the software, copy clustalw.exe and clustalw_help into a CygWin bin directory.

Download information

The original sources can be downloaded here.

The precompiled binary for CygwinB20 and a makefile.diff to apply the above patch to the original sources are shipped as cygwinb20-clustalw1.8.tar.gz (84 kb).