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)
• SeqSphere+ export for GrapeTree for very large MSTs

with more elaborated mitigation of horizontal gene transfer effects

• export concatenated sequences from SeqSphere+
• multiple alignment with MAFFT (Mol Biol Evol. 2013, 30:772)
• ClonalFrameML (PLoS Comput Biol. 2015, 11:e100404), 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, ML & 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

• BEAST (Mol Biol Evol. 2012, 29:1969)
• use as input Gubbins or BRAT-NextGen masked multiple alignments

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.