• VARCall
• FixedVarTools
• GOTools
• iVARCall 1 & iVARCall2

Identification of fixed SNPs and InDels distinguishing homoplastic and non-homoplastic coregenome variants.

VARCall readme

• Identify all comparisons of genome groups referring to all nodes,
• Select sensitive and specific variants,
• Define if these variants are involved the effect of homoplasy.

FixedVAR readme

Gene ontology enrichment analysis based on hypergeometric tests, identifying genome groups and excluding obsolete and non-prokaryotic GO-terms.

GOTools readme

"Independant variant calling". Aims to perform a variant calling analysis from Illumina paired-end reads based on the GATK HaplotypeCaller algorithm. Each sample are processed independently and a g.vcf file is produce for each of them. This allows combination of several iVARCall2 results if the same reference genome is used.

iVARCall readme

iVARCall2 readme

A. Felten, M. Vila Nova, K. Durimel, L. Guillier, M. Mistou and N. Radomski. First gene-ontology enrichment analysis based on bacterial coregenome variants: insights into adaptations of Salmonella serovars to mammalian- and avian-hosts. BMC Microbiology, 2017, 17:222.