Summary on Multiple Alignment Resources on the WWW

Paul St. Amand PST at KSU.KSU.Edu
Thu Mar 9 11:37:36 EST 1995

I didn't see MACAW on your summary. It's a great program available for
Macintosh and Windows. Below is from the file.

Paul St. Amand

Multiple Alignment Construction & Analysis Workbench

MACAW is a program for locating, analyzing, and editing blocks of localized 
sequence similarity among multiple seqences and linking them into a 
composite multiple alignment.


Gregory D. Schuler, Stephen F. Altschul, and David J. Lipman (1991). A 
   Workbench for  Multiple Alignment Construction and Analysis.  Proteins 
   Struct. Funct. Genet. 9, 180-190.

Charles E. Lawrence, Stephen F. Altschul, Mark S. Boguski, Jun S. Liu, Andrew 
   F. Neuwald, and John C. Wootton (1993).  Detecting  Subtle Sequence 
   Signals:  A Gibbs Sampling Strategy for Multiple Alignment.  Science  262, 

Samuel Karlin and Stephen F. Altschul (1990).  Methods for Assessing the 
   Statistical Significance of Molecular Sequence Features by Using General 
   Scoring Schemes. Proc. Natl. Acad. Sci. USA  87, 2264-2268 (1990)


-  From either the Program Manager or the File Manager, run the
   SETUP.EXE program on the diskette.

-  Enter the desired destination directory when prompted to do so.


-  Drag the contents of the diskette to the desired location on
   your hard disk


The program is available for the Macintosh and several flavors of 
Microsoft Windows.  All of them may be downloaded from NCBI's anonymous
FTP server (  Each version is stored in a seperate
directory as described below.

  This directory contains the 16-bit version of MACAW for Windows 3.1x and
  Windows for Workgroups 3.1x.  The file macawz.exe should be downloaded
  in binary mode.

  This directory contains the 32-bit version of MACAW for systems based on
  the Intel family of processors.  It requires either Windows NT or a DOS-hosted
  version of Windows that also has the Win32s subsystem installed.  
  The file macawz.exe should be downloaded in binary mode.

  This directory contains the 32-bit version of MACAW for systems based on
  the DEC Alpha AXP processor and running Windows NT.  The file macawz.exe 
  should be downloaded in binary mode.

  This directory contains the version of MACAW for Macintosh systems based on
  the 680x0 family of processors, but also runs on PowerMacs under emulation.  
  The file macaw.sea.hqx (HexBin format) should be downloaded to your mac.  
  Many Mac FTP programs automatcally convert HexBin files, so you will end 
  up with a file called macaw.sea.  If you do not have such a program, you
  will need to perform HexBin conversion yourself using a utility such as
  Stuffit or Compactor.


-  Download (in BINARY mode) the self-extracting archive 
   file MACAWZ.EXE.

-  At the DOS prompt, type a command like "macawz -d c:\macaw",
   but substituting your preferred destination path.

-  Create an icon for MACAW in the Windows Program Manager.


-  Double-click the macaw.sea icon to launch the program

-  Select the distination folder in the dialog box and press
   the "Extract" button.

    Scientists at the National Center for Biotechnology Information (NCBI) 
develop a variety of computational tools (MACAW is one example) as part of 
their own research and make them available to the scientific community.  
Descriptions of software tools and algorithms are published in appropriate 
journals, and both executables and source code are available upon request from 
the authors.  However, the NCBI cannot provide user support for these tools.  
If you have questions on the use of MACAW, first consult the on-line help 
system as well as the original published sources (see References).  As a last 
resort, you may send e-mail to Greg Schuler (schuler at or 
Stephen Altschul (altschul at, however, you should not expect a 
prompt reply.

Paul C. St. Amand    (PST at KSU.KSU.Edu)
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