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 Parsimony (MP) tree with MEGA or Maximum Likelohood (ML) tree with FastTree (with bootstrap possible)

with more elaborated mitigation of horizontal gene transfer effects

or Gubbins (NAR. 2014, pii:gku1196) masking of recombinatory sites in multiple alignment and ML-tree,
or BRAT-NextGen (NAR. 2012, 40:e6) filtering of polymorphic sites and NJ- & MP trees with MEGA (Mol Biol Evol. 2013, 30:2725)), or ML-tree construction with FastTree (PLoS One. 2010, 5:e9490; Win 32-bit only)

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.