	Parallel Alignment WorkBench

	Installation Manual

1. Directory Configuration

The parallel alignment workbench consists of the following three programs: 

Alignment editor program
Nucleic acid stem part display program
Alignment parallel calculation program

The directory configuration is as shown below.

src ------- unix ------- aedit
       |            |
       |            |
       |            ---- stem
       |
       |
       ---- klic

aedit : Alignment editor program
stem  : Nucleic acid stem part display program
klic  : Alignment parallel calculation program


2. Execution Environment for Each Program}

Alignment editor program 

Machine     : UNIX workstation
Environment : UNIX,XWindow,OFS/Motif,cc(gcc)
Language    : C
Source Code : 1.6MB


Nucleic acid stem part display program

Machine     : UNIX workstation
Environment : UNIX,XWindow,OFS/Motif,cc(gcc)
Language    : C
Source Code : 190KB


Alignment parallel calculation program

Machine     : UNIX base parallel calculation machine
Environment : UNIX,KLIC,gcc(cc)
Language    : KL1,C
Source Code : 650KB


3. Installation Method for Each Program

Nucleic acid stem part display program

 (1) Place ./src/unix/stem/* on the same directory under UNIX .

 (2) Copy appropriate Makefile.* to Makefile .
     For example, if you are going to use this program on Indigo,
     type  " cp Makefile.indigo Makefile" .

 (3) Execute "make". Then, the executable file "ste" will be generated.


Alignment editor program

 (1) Place ./src/unix/aedit/* on the same directory under UNIX .

 (2) Copy appropriate Makefile.* to Makefile .
     For example, if you are going to use this program on Solaris,
     type  " cp Makefile.solaris Makefile" .

 (3) Execute "make". Then, the executable file "aedit" will be generated.

 (4) Use of the programs require some files.

     aedit.res    -> Copy the file to the current directory, or the directory set by set path.

     prosite.dat
     user.dat     -> Copy the files to the current directory, or the directory set by setenv 
                     AEDIT_MOTIF_DIR.

     ste          -> Copy the file to the current directory, or the directory set by set path.

     original.clr -> Copy the file to the current directory.


Alignment parallel calculation program

 (1) Place ./src/klic/* on the same directory on a UNIX-base parallel
     machine to which KLIC is ported.

 (2) Refer to `compile' and execute `klic' to perform compilation. 
     Then, the executable file `align_p' generates.


4. How to Use Each Program

Alignment editor program

 See the  ``Alignment Editor Program GUI Operation Manual''  stored on a separate file.


Nucleic acid stem part display program

 See the ``Nucleic Acid Stem Part Display Program GUI Operation
 Manual'' stored on a separate file.


Alignment parallel calculation program

 See the ``Alignment Parallel Calculation Program Operation Manual''
 stored on a separate file.
