
\paragraph{prokaryote}
In~\cite{SMMR+13}, the authors compare some smooth tubercle baciles isolates
with M. tuberculosis regarding 
branching, core genome,
genome sizes, and 
number of scars.
To achieve this, the authors 
\begin{enumerate} 
\item compare the hamming distance and the bootstrap probability between 12 gene segments;
\item compute pairwise comparisons of some selected SNPs data;
\item use NeighborNet analysis, based on pairwise alignments of some selected 
  SNPs data.
\end{enumerate}

In~\cite{10.1371/journal.pone.0052841} the authors analyse 435 Mycobacterium Tuberculosis complex isolates of the same clade. By focusing on the H37Rv genome, 
they produce 13382 SNPs. Later, they  compare  44 genomes to this one 
regarding these SNP. The way they extract this phylogenetical tree is 
not detailed. They focus then on Percy256 and Percy556 since both these 
genomes have a very long branch split from the  M. Canetti. They deduce then 
a new lineage.



\paragraph{eukaryote}
In~\cite{CGOT10}, the authors show how to reconstruct an ancestral genome of seven eukaryotes species (Saccharomyces cerevisiae, Candida glabrata, Zygosaccharomyces rouxii, Kluyveromyces lactis, Ashbya gossypii, Kluyveromyces thermotolerans, Saccharomyces kluyveri).
Their method is as follows:
\begin{enumerate}
\item the starting point is a set of markers covering a large
  part of the extant genomes and which are believed to
  be present in a unique exemplar in the ancestral genome.
\item first method: rearrangement methods and particularely median method. Authors even provide informations about medians in case of duplicated genomes or not.   
\item second method: physical mapping techniques by trying to guess
  which genes should be close to each other, 
  and propose a mapping that maximize an objective function.
\end{enumerate}
