======================== AUTHORS =========================

Wojciech Frohmberg      wojciech.frohmberg [at] cs.put.poznan.pl
Michał Kierzynka        michal.kierzynka [at] cs.put.poznan.pl


====================== INSTALLATION ======================

Installation (non-interactive mode, without MPI support):

tar zxf gdna.tar.gz
cd gdna/
./configure
make
sudo make install

Installation (with interactive mode, without MPI support):

tar zxf gdna.tar.gz
cd gdna/
./configure --default-no
(here comes interactive questions e.g. where to install application etc.)
make
make install

Installation (with MPI support):

tar zxf gdna.tar.gz
cd gdna/
./configure --mpi
make
sudo make install


If something goes wrong in the process of ./configure try
to install missing dependencies (the script should suggest
what is missing) before running the ./configure script
with desired parameter, type:

./configure --clean

=========================== USE ===========================

Example use of the application:
./gdna --alg nws -sm data/sm/own4.sm --seqs data/fasta/454.fasta --pairs data/pairs/454.pairs --gap-penalty 1 --pairs-per-gpu 8192 --results out.txt

In the example above the results are written to out.txt text
file in the following format:
id_of_the_first_sequence id_of_the_second_sequence score overlap

Hint: operating on files is not always very efficient,
especially if you play with big data. Hence, it is
suggested to incorporate gdna into your own software
code. Feel free to do this, after contacting us
first - see "TERMS OF USE".


To get familiar with custom options of the application type:
./gdna --help

======================= TERMS OF USE =======================

The software is provided "as is".
The authors do not guarantee that the software is free of bugs
In no event shall the authors be liable for any damages of any kind. 

If you use the software in your research please contact us.



