Main tool: kSNP4 https://sourceforge.net/projects/ksnp/files/
Additional tools: None
Full documentation: https://sourceforge.net/projects/ksnp/files/kSNP4%20User%20Guide.pdf/download
Summary:
kSNP4 is a program that identifies the pan-genome SNPs in a set of genome sequences, and estimates phylogenetic trees based upon those SNPs. Because there are many potential downstream applications of SNP information, kSNP4 also provides output files that include a multiple alignment of all of the SNP positions and files that provide information about the positions of each SNP in each genome and annotations. kSNP4 can analyze both complete (finished) genomes and unfinished genomes in assembled contigs or raw, unassembled reads. Finished and unfinished genomes can be analyzed together, and kSNP4 can automatically download Genbank files of the finished genomes (and annotated genome assemblies) and incorporate the information in those files into the SNP annotation. Core SNPs, those present in all of the genomes, can optionally be analyzed separately to generate a multiple SNP alignment and trees based on only the core SNPs. kSNP4 also can provide a separate analysis of those SNPS that occur in at least a user-determined fraction of the genomes.
kSNP4 -in Eco100.in -k 21 -outdir Run1 -annotate annotatedGenomes