I did something similar recently using my custom terminal diff tool. Here is a more colourful terminal-based view of the differences between MN908947.3 and sar

I did something similar recently using my custom terminal diff tool. Here is a more colourful terminal-based view of the differences between MN908947.3 and sars NC_004718.3: https://twitter.com/RobertElderSoft/status/1222690629492379649/photo/1 https://twitter.com/RobertElderSoft/status/12226906294923796... To produce that image I used this tool: https://github.com/RobertElderSoftware/roberteldersoftwarediff https://github.com/RobertElderSoftware/roberteldersoftwaredi... With these two genomes: https://www.ncbi.nlm.nih.gov/nuccore/MN908947 https://www.ncbi.nlm.nih.gov/nuccore/MN908947 https://www.ncbi.nlm.nih.gov/nuccore/NC_004718.3 https://www.ncbi.nlm.nih.gov/nuccore/NC_004718.3 with the leading numbers, spaces and newlines removed from each genome file. My tool (as well as unix diff with --minimal) uses the myers diff algorithm which just compute a mathematically minimal diff. More advanced algorithms exist for computing phylogenetic trees that take into account the biological likelihood of certain sequence change (deletions vs. additions vs. translations etc.).