This is the Linux app named kSNP whose latest release can be downloaded as kSNP4.1-source-code.zip. It can be run online in the free hosting provider OnWorks for workstations.
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kSNP
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DESCRIPTION
kSNP4 identifies the pan-genome SNPs in a set of genome sequences, and estimates phylogenetic trees based upon those SNPs. SNP discovery is based on k-mer analysis, and requires no multiple sequence alignment or the selection of a reference genome, so kSNP4 can take 100's of microbial genomes as input. A SNP locus is defined by an oligo of length k surrounding a central SNP allele. 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 kSNP can automatically download Genbank files of the finished genomes and incorporate the information in those files into the SNP annotation.
No programming skills are required to use kSNP4
Gardner, S.N. and Hall, B.G. 2013. . PLoS ONE, 8(12):e81760.doi:10.1371/journal.pone.0081760
Gardner, S.N., T. Slezak, and B.G. Hall. 2015 Bioinformatics 31: 2877-2878 doi: 10.1093/bioinformatics/btv271
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This is an application that can also be fetched from https://sourceforge.net/projects/ksnp/. It has been hosted in OnWorks in order to be run online in an easiest way from one of our free Operative Systems.
