Hello everyone... I am currently working on SNP identification between wild boar and domestic pigs with nuclear genome level. I am using progressive Mauve for whole genome alignment and Geneious prime for the SNP identification. Progressive Mauve is not aligning the end to end and Geneious prime couldn't handle SNP calling for large MSA files. So I am looking for an alternative workflow for whole genome alignment and SNP identification. Kindly suggest a workflow or tool for this study. Computer specification: intel i9 processor with 64 GB RAM (ubuntu / Windows 11 os).