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seq++ is free software library; you can redistribute it and/or modify it under
the terms of the GNU General Public License as published by the Free Software
Foundation;  either version 2 of the License, or (at your option) any later 
version.
This program is distributed in the hope that it will be useful, but 
WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
General Public License for more details.

You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA.
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The object-oriented library seq++ offers a C++ reference toolkit 
for developers working on sequences and statistics. The package contains also
estimation and simulation programs to be installed as binairies. The genericity of seq++
is ensured by the possibility of storing and working with any kind of 
sequence based on any alphabet (DNA, proteins, codons, others...). seq++ 
enables to model sequences with Markov, Variable Length Markov and newly 
developped Parsimonious Markov models. All these models may be phased. 
Markovian simulations are implemented so that developers can 
perform Monte Carlo methods. 

NOTICE: The following procedure installs on your system both the library as a shared library and associated include files
and the binairies such as estimation and simulation programs.

0/ Requirements : compilators C++ and F77, library GSL and XML2(optionnal).

1/ the installation procedure is explained in ./INSTALL.
The classical way, compliant with the GNU standard procedure:
- ./configure  (add "--enable-xml" to activate xml options, libxml2 required)
- make
- make check
- make install
- make docs (if you want to generate the html doc)

NB: for a debug compilation, add "--enable-debug and then le library name becomes "seqpp_g"

2/ you can then include files from seqpp by such an include
exple: #include <seqpp/.....>

2'/ you can then use the binary programs.
exple: estim_m --help

3/ you now must compile with the -lseqpp
or use in your configure.in the set of instructions :
AC_CHECK_LIB( seqpp, main )

4/ don't forget to fit your $LD_LIBRARY_PATH for the linkage

5/ please watch the TODO file which explains the current developements.

6/ Bug report:
If you experiment any bug with seq++, please send a mail to miele@genopole.cnrs.fr with the following subject "bug report". At last, feel free to add any relevant comments to that bug report. We will try to answer to most of those reports.
Other feedback:
seq++ is an emerging project which is still in evolution. Thus, your feedback are more than welcome to help us to get seq++ better than it is. For any suggestion or comment, please send a mail to miele@genopole.cnrs.fr with the following subject "feedback".

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- Vincent Miele (miele@genopole.cnrs.fr) -
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