This community developed web-service aims at simplyfing and standardizing the benchmarking of alignment-free tools. And for the users, the benchmarks provide a way to identify the most effective methods for the problem at hand.

Core SNPs exclude loci that are distinguishable within some clades but absent in others. Core SNPs will not cover mutations from regions deleted in a branch of the tree, or SNPs in horizontally transferred genes present in a subset of genomes.

Several methods for whole-genome SNP discovery or phylogenetics have been described: SNPsFinder(Song et al. 2005), PhyloSNP(Faison et al. 2014), kSNP(Gardner and Hall 2013), WG-FAST(Sahl et al. 2015), and CFSAN(Davis et al. 2015). SNPsFinder requires assembled genomes, uses the time-consuming megaBLAST program, and only provides a table of identified SNPs. PhyloSNP requires pre-aligned data (such as vcf files or tab-delimited lists of SNPs), does not scale to large datasets, and only produces maximum parsimony trees based on the presence or absence of SNPs. Like PhaME, kSNP, WG-FAST, and CFSAN can analyze raw reads to identify a core genome (the conserved portion among all genomes). However kSNP is restricted to finding central SNPs within an optimal kmer window, the size of which must first be provided by the user and influences the resulting tree. WG-FAST is a rapid method that identifies the most closely related known genome for given input data, but requires a pre-formatted SNP matrix of known SNP positions for a target organism and a pre-computed phylogeny. CFSAN aligns read datasets against a designated reference genome to generate a SNP matrix, but only allows the inclusion of a single reference genome and does not build phylogenies. Because each of these pipelines perform only part of the steps required to infer phylogenies from a particular form of sequencing data (i.e. either reads or contigs), we have developed an integrated PhaME analysis pipeline which provides rapid tree construction from assemblies and reads and downstream evolutionary analysis of functional genes, with the ability to incorporate pre-constructed alignments and phylogenies.