snpTree server implementation. (A) SNP tree construction from raw reads. Pre-processing (shown in blue) filters and trims raw data to remove low-quality bases. Trimmed raw reads are aligned against a reference genome by BWA with mapping quality equal to 30 as a default. SNPs calling and filtering process (shown in purple) identifies and filters informative SNPs by SAMtools with a couple of cut-offs, minimum coverage and minimum distance between each SNP (the default for both cut-offs is 10) and additionally all heterozygote SNPs are filtered. SNPs tree construction step (shown in orange) transforms from multiple alignments of concatenated SNPs to a phylogenetic tree by using Fastree and a perl script. (B) SNP tree construction from assembled genomes. Contigs or assembled genome are aligned to a reference genome using Nucmer. The SNPs calling and SNPs filtering steps are performed by a 'show-snps' application from MUMmer. SNPs tree construction step is carried out as the same way as the raw reads.