Multipule Sequence Alignment Program by using Parallel Iterative Method (with KLIC)


Directory Configuration

Please see README on each directory.

pia_kilc ----- Alignment ----- parallel(klic)
           |               |
           |               --- sequential(c)
           |               
           --- WorkBench ----- src ----- klic
                           |         |
                           |         --- unix ----- aedit
                           |                    |
                           |                    --- stem
                           |
                           --- manual ----- english
                                        |
                                        --- japanese

1) Alignment

Multipule Sequence Alignment Programs by using Iterative Method


These programs are executed by unix command line.
There are two directories. One used with parallel machine,
and the other used with sequential machine.
Please see README on each directory.


Environment

parallel   -> Machine     : Parallel machin based on UNIX
              Environment : KLIC,UNIX,gcc(cc)
              Language    : KL1,C
              Source Code : 190KB
              
sequential -> Machine     : UNIX workstation
              Environment : UNIX,cc(gcc)
              Language    : C
              Source Code : 2.1MB


2) WorkBench

Parallel Alignment WorkBench


This program has a good GUI and several features.

Constraint-based aligners automatically align the user-specified regions.
You can use a parallel machine via network, 
when the large amount of computation is required.

Equipped with motif dictionaries such as PROSITE, this editor searches
the aligned sequences for motifs.
When motifs are searched for,those regions are shown.
User-defined dictionary is also available.

A phylogenetic tree drawer is available by using UPGMA method and NJ method,
when we want to know the evolutional relation of the sequences.

Only using a pointing device, we can edit a sequence alignment
speedily and comfortably. 
Insert gaps and delete gaps. 
Fixing a column of alignment.

The stem specifier indicates some possible stacking regions
in an RNA sequence alignment by using a circle representation of the
secondary RNA structure.


The parallel alignment workbench consists of the following three programs: 

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


Environment

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

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

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