--- /dev/null
+@article{SMMR+13,
+title={Genomic analysis of smooth tubercle bacilli provides insights into ancestry and pathoadaptation of Mycobacterium tuberculosis},
+url={http://www.nature.com/ng/journal/v45/n2/full/ng.2517.html},
+DOI={10.1038/ng.2517},
+volume={45},
+number={2},
+journal={Nature Genetics},
+author={Philip Supply and Michael Marceau and Sophie Mangenot and David Roche and Carine Rouanet and Varun Khanna and Laleh Majlessi and Alexis Criscuolo and Julien Tap and Alexandre Pawlik},
+year={2013},
+ pages={172–179}}
+
+@article{CGOT10,
+title={Yeast Ancestral Genome Reconstructions: The Possibilities of Computational Methods II},
+author={Cedric Chauve and Haris Gavranovic and Aida Ouangraoua and Eric Tannier},
+journal={Journal of Computational Biology},
+month=sep,
+year={2010},
+volume=17,
+number=9,
+pages={1097--1112},
+DOI={10.1089/cmb.2010.0092}
+}
+
+@incollection{FI09,
+year={2009},
+isbn={978-3-642-04743-5},
+booktitle={Comparative Genomics},
+volume={5817},
+series={Lecture Notes in Computer Science},
+editor={Ciccarelli, FrancescaD. and Miklós, István},
+doi={10.1007/978-3-642-04744-2_1},
+title={Yeast Ancestral Genome Reconstructions: The Possibilities of Computational Methods},
+url={http://dx.doi.org/10.1007/978-3-642-04744-2_1},
+publisher={Springer Berlin Heidelberg},
+author={Tannier, Eric},
+pages={1-12}
+}
+
+
+@article{10.1371/journal.pone.0052841,
+ author = {Blouin, Yann AND Hauck, Yolande AND Soler, Charles AND Fabre, Michel AND Vong, Rithy AND Dehan, Céline AND Cazajous, Géraldine AND Massoure, Pierre-Laurent AND Kraemer, Philippe AND Jenkins, Akinbowale AND Garnotel, Eric AND Pourcel, Christine AND Vergnaud, Gilles},
+ journal = {PLoS ONE},
+ publisher = {Public Library of Science},
+ title = {Significance of the Identification in the Horn of Africa of an Exceptionally Deep Branching <italic>Mycobacterium tuberculosis</italic> Clade},
+ year = {2012},
+ month = {12},
+ volume = {7},
+ url = {http://dx.doi.org/10.1371%2Fjournal.pone.0052841},
+ pages = {e52841},
+ abstract = {<p>Molecular and phylogeographic studies have led to the definition within the <italic>Mycobacterium tuberculosis</italic> complex (MTBC) of a number of geotypes and ecotypes showing a preferential geographic location or host preference. The MTBC is thought to have emerged in Africa, most likely the Horn of Africa, and to have spread worldwide with human migrations. Under this assumption, there is a possibility that unknown deep branching lineages are present in this region. We genotyped by spoligotyping and multiple locus variable number of tandem repeats (VNTR) analysis (MLVA) 435 MTBC isolates recovered from patients. Four hundred and eleven isolates were collected in the Republic of Djibouti over a 12 year period, with the other 24 isolates originating from neighbouring countries. All major <italic>M. tuberculosis</italic> lineages were identified, with only two <italic>M. africanum</italic> and one <italic>M. bovis</italic> isolates. Upon comparison with typing data of worldwide origin we observed that several isolates showed clustering characteristics compatible with new deep branching. Whole genome sequencing (WGS) of seven isolates and comparison with available WGS data from 38 genomes distributed in the different lineages confirms the identification of ancestral nodes for several clades and most importantly of one new lineage, here referred to as lineage 7. Investigation of specific deletions confirms the novelty of this lineage, and analysis of its precise phylogenetic position indicates that the other three superlineages constituting the MTBC emerged independently but within a relatively short timeframe from the Horn of Africa. The availability of such strains compared to the predominant lineages and sharing very ancient ancestry will open new avenues for identifying some of the genetic factors responsible for the success of the modern lineages. Additional deep branching lineages may be readily and efficiently identified by large-scale MLVA screening of isolates from sub-Saharan African countries followed by WGS analysis of a few selected isolates.</p>},
+ number = {12},
+ doi = {10.1371/journal.pone.0052841}
+}
+@Article{17623808,
+AUTHOR = {Gomez-Valero, Laura and Rocha, Eduardo P C and Latorre, Amparo and Silva, Francisco J},
+TITLE = {Reconstructing the ancestor of Mycobacterium leprae: the dynamics of gene loss and genome reduction.},
+JOURNAL = {Genome Res},
+VOLUME = {17},
+YEAR = {2007},
+NUMBER = {8},
+PAGES = {1178-85},
+URL = {http://www.biomedsearch.com/nih/Reconstructing-ancestor-Mycobacterium-leprae-dynamics/17623808.html},
+PubMedID = {17623808},
+ISSN = {1088-9051}
+}
\ No newline at end of file
--- /dev/null
+This step considers as input the set
+$\{((g_1,g_2),r_{12}), (g_1,g_3),r_{13}), (g_{n-1},g{n}),r_{n-1.n})\}$ of
+$\frac{n(n-1)}{2}$ elements.
+Each one $(g_i,g_j),r_{ij})$ where $i < j$,
+is a pair that gives the similarity rate $r_{ij}$ between the two genes
+$g_{i}$ and $g_{j}$.
+
+The first step of this stage consists in building the following non-oriented
+graph further denoted as to \emph{similarity graph}.
+In this one, the vertices are the genes. There is an edge between
+$g_{i}$ and $g_{j}$ if the rate $r_{ij}$ is greater than a given similarity
+threshold $t$.
+
+We then define the relation $\sim$ such that
+$ x \sim y$ if $x$ and $y$ belong in the same connected component.
+Mathematically speaking, it is obvious that this
+defines an equivalence relation.
+Let $\dot{x}= \{y | x \sim y\}$
+denotes the equivalence class to which $x$ belongs.
+All the genes which are equivalent to each other
+are also elements of the same equivalence class.
+Let us then consider the set of all equivalence classes of the set of genes
+by $\sim$, denoted $X/\sim = \{\dot{x} | x \textrm{ is a gene}\}$.
+defined by $\pi(x) = \dot{x}$
+which maps each gene into it respective equivalence class by $\sim$.
+
+
+
+
+For each genome $[g_l,\ldots,g{l+m}]$, the second step computes
+the projection of each gene according to $\pi$.
+The resulting genome which is
+$$
+[\pi(g_l),\ldots,\pi(g{l+m})]
+$$
+is again of size $m$.
+
+Intuitively speaking, for two genes $g_i$ and $g_j$
+in the same equivalence class, there is path from $g_i$ and $g_j$.
+It signifies that each evolution step
+(represented by an edge in the similarity graph)
+has produced a gene s.t. the similarity with the previous one
+is greater than $t$.
+Genes $g_i$ and $g_j$ may thus have a common ancestor.
+
+
+We compute the core genome as follow.
+Each genome is projected according to $\pi$. We then consider the
+intersection of all the projected genomes which are considered as sets of genes
+and not as sequences of genes.
+This results as the set of all the class $\dot{x}$
+such that each genome has an gene $x$ in $\dot{x}$.
+The pan genome is computed similarly: the union of all the
+projected genomes in computed here.
+
--- /dev/null
+\documentclass{article}
+\usepackage{subfig}
+\usepackage{color}
+\usepackage{graphicx}
+\usepackage{url}
+\usepackage{cite}
+
+% correct bad hyphenation here
+\hyphenation{op-tical net-works semi-conduc-tor}
+
+
+\begin{document}
+\title{Finding the core-genes of Chloroplast Species}
+
+
+\author{
+Bassam Al-Kindy,
+Jean-Fran\c{c}ois Couchot,
+Christophe Guyeux,
+and Michel Salomon*\\
+ FEMTO-ST Institute, UMR 6174 CNRS\\
+ Computer Science Laboratory DISC,
+ University of Franche-Comt\'{e},
+ Besan\c con, France.\\
+ $*:$ Authors in alphabetic order.\\
+}
+\newcommand{\JFC}[1]{\begin{color}{green}\textit{}\end{color}}
+\newcommand{\CG}[1]{\begin{color}{blue}\textit{}\end{color}}
+% make the title area
+\maketitle
+
+
+
+
+%IEEEtran, journal, \LaTeX, paper, template.
+
+\maketitle
+
+\begin{abstract}
+\end{abstract}
+
+
+
+
+
+
+
+
+\section{Introduction}\label{sec:intro}
+%\input{intro.tex}
+
+
+\section{Similarity-based Approach }
+%input
+% Main author : jfc
+\input{classEquiv}
+
+
+
+\section{Annotated-based Approach}
+% Main author : bassam
+
+
+
+
+
+
+% \section{Second Stage: to Find Closed Genomes}
+% \input{closedgenomes}
+
+
+\section{Conclusion}\label{sec:concl}
+
+
+\bibliographystyle{plain}
+\bibliography{biblio}
+
+
+
+\end{document}
+
+
