ContentsDe-novo Assembly BasedCore or core & accessory genome gene SNP phylogenywith simple mitigation of horizontal gene transfer effects
with more elaborated mitigation of horizontal gene transfer effects
Whole genome SNP phylogeny
Bayesian phylogenetic inference, divergence time dating, coalescent analysis and/or phylogeography analysis
Mapping BasedBwa 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. |