\begin{abstract}
\color{red}Investigating in the evolution of genomes become a hard task due to the amount of evolutionary techniques and the amount of genomes that raises every day. The important question to understand here is: how can we clusterize large amounts of chloroplast species?, and what are the common genes that play a role in the process of evolution among these species?. Clusterizing collection of species aims to find the common genes that share the same functionality properties. In other words, clustering helps us to find the core and pan genome among species that share a common properties, such us gene name, gene sequence, family, \dots, etc. According to other studies, finding such core and/or pan genome is not an easy task due to a large amount of computation, and requiring a rigorous methodology. \color{black}
%Due to the recent evolution of sequencing techniques, the number of
%available genomes is rising steadily, raising the problem to determine
%what to do with such large sets of DNA data. An interesting question
%is to understand what are the common functionality of a collection
%of species or, conversely, to determine what is specific to a given
%species when compared to other ones belonging in the same genus, family, etc.
%Investigating such a problem means to find both core and pan genomes
%of a collection of species, that is, genes in common to all the species
%vs. genes present at least once in the set of genomes. However, to obtain
%trustworthy core and pan genomes is not an easy task, leading to a large 
%amount of computation, and requiring a rigorous methodology. Surprisingly,
%as far as we know, this methodology in finding core and pan genomes has not really been
%investigated in detail. This research work tries to fill this gap
%by focusing only on chloroplastic genomes, whose reasonable sizes allow a deep study.
%% DNA analysis  techniques have received  a lot of attention  these last
%% years, because  they play an  important role in  understanding genomes
%% evolution over time, and in phylogenetic and genetic analyses. 
%% However systematic approaches to determine 
%% %Various
%%models  of  genomes  evolution  are  based  on  the  analysis  of  DNA
%%sequences, SNPs,  mutations, and so on. 
To achieve this goal, a collection of 99 chloroplasts are 
considered in this article. Two methodologies will be 
investigated, respectively based on sequence similarities and 
%genes names taken 
from annotation tools.
The obtained results will finally be evaluated in terms of performances and 
biological relevance.
% Various  genes prediction methods will be
% firstly compared, some of them being specific to chloroplastic genomes. 
% Then clustering methods will be proposed and evaluated, in order
% to group these coding sequences by orthologous genes.
% % We  have recently investigated
% the use of  core (\emph{i.e.}, common genes) and  pan genomes to infer
% evolutionary  information  on  a  collection of  99~chloroplasts.   In
% particular,  we  have  regarded  methods  to  build  a  genes  content
% evolutionary  tree  using  distances  to core  genome.   However,  the
% production of reliable  core and pan genomes is not  an easy task, due
% to error  annotations. The aim of this methodology article is to 
% % investigate various ways to .
% We will  first compare different  approaches to
% construct such a tree using fully annotated genomes provided by NCBI and
% DOGMA, followed by a gene quality control among the common genes. Then
% we  will explain  how, by  comparing  sequences from  DOGMA with  NCBI
% contents, we  achieved to identify the  genes that play a  key role in
% the dynamics of genomes evolution.

\textbf{Keywords:} Core genome, Methodology, Pan genome, Genes prediction, Coding sequences clustering, Chloroplasts, Gene quality test. 
\end{abstract}
