      Parallel Alignment WorkBench


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. Overview of Each Program

2.1. Alignment Editor Program

The alignment editor program is the main program of the parallelalignment workbench.

The nucleic acid stem part display program and the alignment parallel
calculation program are called from the alignment editor program. 
The alignment editor program can also be used alone.

The followings are the representative functions of the alignment editor program.

* The program can edit insertion and deletion of gaps by using only a mouse. 

* The program can insert, delete, and overwrite the amino acid, nucleic acid, and gap.

* The program can write evolution trees.

* The program can retrieve motifs in a display alignment from the
  Prosite or user-defined database (Prosite format).

* The program can call the nucleic acid stem part display program.

* The program can perform the sequential algorithm alignment
  calculation internally and locally on the started machine.

* The program can call the parallel algorithm alignment calculation
  program to perform calculation on the parallel computers.

* The program can reflect constraints (parts that must be aligned
  vertically) to the alignment calculation.

* Other functions

For details, refer to the  ``Alignment Editor Program GUI Operation Manual.''   


2.2. Nucleic Acid Stem Part Display Program

The nucleic acid stem part display program checks if base pairs are
made between columns within the nucleic acid alignment. When the ratio
of the number of arrays in which base pairs are made against the total
number of arrays between columns within the alignment exceeds the
specified percentage, the program assumes that base pairs are made
between the columns. And, when the number of continuous columns in
which base pairs are made exceeds the specified number of columns, the
program displays those continuous columns as a mutually complementary
base array part that has a high possibility of being stored.

For details, refer to the  ``Nucleic Acid Stem Part Display Program GUI Operation Manual.''  


2.3. Alignment Parallel Calculation Program

The alignment parallel calculation program performs alignment
calculation on parallel computers.

For details, refer to the ``Alignment Parallel Calculation Operation
Manual'' and the ``Explanation on the Alignment Algorithm'' which are
stored on separate files.


3. 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


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.
