[Parsnp]

   Treangen TJ*, Ondov BD*, Koren S, Phillippy AM:
     The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes.
     Genome Biology (2014). doi: http://dx.doi.org/10.1186/s13059-014-0524-x

* These authors contributed equally to this work

External software (please also cite if you find Parsnp useful):

   [FastTree2]
   
      Price MN, Dehal PS, Arkin AP: 
        FastTree 2--approximately maximum-likelihood trees for large alignments. 
        PLoS One 2010, 5:e9490.
   
   [Muscle]
   
      Edgar RC:
        MUSCLE: multiple sequence alignment with high accuracy and high throughput. 
        Nucleic Acids Research 2004, 32:1792-1797.
   
   [PhiPack]

      Bruen TC, Philippe H, Bryant D: 
        A simple and robust statistical test for detecting the presence of recombination. 
        Genetics 2006, 172:2665-2681.
    
    
