Fig. 1

a Example output figure from Synima. Synteny is shown in the default R colour azure4 for four genomes representing each of the four lineages of the pathogenic fungus Cryptococcus gattii [16]. Isolate names are shown to the right of their genomes, which are represented by lines, with vertical lines indicating chromosomal/scaffold/contig borders, and their identifiers listed above (sc = supercontig, +/− = orientation). Supercontig (sc) 5 of the hypervirulent VGII CNB2/R265 isolate and sc1 of VGIV IND107 are highlighted in R colours ‘darkgoldenrod1’ and ‘cadetblue’, respectively. Genes involved in 1) ergosterol production, 2) capsule biosynthesis and 3) capsule attachment and cell wall remodeling [26] are shown as boxes in R colours ‘cornflowerblue’, ‘coral3’ and ‘darkcyan’, respectively. Sc’s and genes highlighted are for illustrative purposes only. The ordering and orientation of chromosomes are automatically calculated and applied by Synima, although manual changes to these can be made in the config file, e.g. re-orienting sc1 in IND107 (highlighted), CA1280 sc2 and WM276 cgba to avoid synteny overlap across the four genomes. b Mummer 3.22 alignment and Dotplot for C. gattii VGII CNB2/R265 vs C. gattii VGIV IND107. c Circos v0.66 figure of C. gattii VGII CNB2/R265 vs C. gattii VGIV IND107, ordered according to Synima’s pipeline