De-novo Assembly Based

Core or core & accessory genome gene SNP phylogeny

with simple mitigation of horizontal gene transfer effects

  • SeqSphere+ SNP minimum spanning (MST) or Neighbor-Joining trees (NJ-trees) (no bootstrap support)
  • SeqSphere+ export of concatenated SNPs and Maximum Likelohood (ML) or Maximum Parsimony (MP) tree with MEGA X or ML tree with FastTree (all with bootstrap possible)

with more elaborated mitigation of horizontal gene transfer effects

Whole genome SNP phylogeny

  • multiple alignment of de novo assemblies with progressiveMauve (PLoS One. 2010, 5:e11147)
  • optional: Gubbins or BRAT-NextGen masking of recombinatory sites in multiple alignment
  • MEGA or FastTree MP- or ML-trees

Bayesian phylogenetic inference, divergence time dating, coalescent analysis and/or phylogeography analysis

Mapping Based

Bwa mapping against one reference and GATK/VarScan (Genome Res. 2012, 22:568) SNP calling. However, exclusion of non-polymorphic SNPs and the alignment to a single reference genome introduces systematic biases. Therefore, REALPHY (Mol Biol Evol. 2014, 31:1077) combines alignments from mappings to multiple references and uses also non-polymorphic SNPs for tree building. Gubbins or BRAT-NextGen masked multiple alignments as input for FastTree ML or BEAST Bayesian tree building.