PhyML is a statistical analysis software that allows to trace the evolution of genes and sometimes even complete genomes. 56 genomes of the Coronavirus nCov-2019 are available to date (February 4, 2020).
The reconstruction of the phylogenetic tree of these viruses (i.e. their genealogy) by PhyML has shown (1,2) that a first group of individuals was contaminated in December 2019 in Wuhan, following a single zoonosis event, i.e. transmission of the virus from animals to humans. Phylogenetic analysis also confirmed that the subsequent transmissions were human-to-human, thus ruling out the hypothesis of multiple transmissions from a pool of infected animals.
PhyML is a software designed and developed by Stéphane Guindon and the LIRMM bioinformatics team. The articles (3,4) describing the algorithms implemented in this tool total more than 25,000 citations.”

Links :
(1)http://virological.org/t/phylodynamic-analysis-56-genomes-05-feb-2020/356
(2)http://virological.org/t/temporal-signal-and-the-evolutionary-rate-of-2019-n-cov-using-47-genomes-collected-by-feb-01-2020/379
(3)https://academic.oup.com/sysbio/article/52/5/696/1681984
(4)https://academic.oup.com/sysbio/article/59/3/307/1702850
(5)https://ins2i.cnrs.fr/fr/cnrsinfo/phyml-un-logiciel-pour-remonter-la-piste-du-coronavirus