Clustal W is a sequence alignment tool for nucleic acid sequences:
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
The CygWin port is based on Clustal W version 1.8.
The source code is ANSI C and compiles with gcc, so it took
only minor modifications in the makefile to compile on
The first part of the diff eliminates two tabs that GNU make
complains about. The second part sets the c compiler to
--- /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 @@
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
I used the following setup to build the software:
- Windows NT 4.0 SP3 Workstation
With this setup,
make gives a clean build.
To install the software, copy clustalw.exe and clustalw_help
into a CygWin bin directory.
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).