
The last stage of the proposed pipeline is naturally to take advantage
of the produced core and pan genomes for biological studies. As
this key stage is not directly related to the methodology for core
and pan genomes discovery, we will only outline a few tasks that
can be operated on the produced data.

%\begin{figure}
%\centering
%\includegraphics[scale=0.215]{tree}
%\caption{Part of a core genomes evolutionary tree (NCBI gene names)}
%\label{coreTree}
%\end{figure}

Obtained results may be visualized by building a core genomes evolutionary tree. 
% All core  genes generated  represent  an important information  in the  tree,
% because they  provide ancestor information of two  or more
% genomes. 
Each  node in this  tree represents a chloroplast  genome or
a predicted core. %, as depicted in Figure~\ref{coreTree}. In this figure, nodes labels are of the form \textit{(Genes number:Family name\_Scientific name\_Accession number)},while an edge is labeled with the number of gene loss when compared to its parents (a leaf  genome or  an intermediate core  genome). Such numbers can answer questions like: how many genes are different between two  species? Which functionality has been lost between an ancestor and its children ? For complete core treesbased either on NCBI names or on DOGMA ones, see supplementary data.

A second application of such data is obviously to build accurate phylogenetic   
trees, using tools like
PHYML\cite{guindon2005phyml} or 
RAxML{\cite{stamatakis2008raxml,stamatakis2005raxml}. 
Consider a set of species, the last common core genome in the core tree 
contains all the genes shared in common by these species. These genes may be
multi aligned to serve as input of the phylogenetic tools mentioned above.
An example of such a phylogenetic tree on core 58 (NCBI cores tree, see
supplementary data) is provided in Appendix~\ref{philoTree}. Remark that, in
order to constitute a relevant outgroup, we have simply blasted each gene 
of this core on a chosen \emph{Cyanobacteria}.


%,    BioNJ,    and
%TNT\cite{goloboff2008tnt}}.    
% In   this  work,   we   chose  to   use
% RAxML\cite{stamatakis2008raxml,stamatakis2005raxml}   because   it  is
% fast, accurate,  and can build large  trees when dealing  with a large
% number of genomic sequences.
% 
% The procedure used to built a phylogenetic tree is as follows:
% \begin{enumerate}
% \item For each gene in a core gene, extract its sequence and store it in the database.
% \item Use multiple alignment tools such as (****to be write after see christophe****) 
% to align these sequences with each others.
% \item Use an outer-group genome from cyanobacteria to calculate distances.
% \item Submit the resulting aligned sequences to RAxML program to compute 
% the distances and finally draw the phylogenetic tree.
% \end{enumerate} 
% 


