Thanks Mensur,

I have meticulously followed the installation instructions for these tools. But yes, perhaps I should instead have asked if anyone would have a working script for installing any of these programs in Linux. If I fail to install MUMmer as well, I will follow your advice :). Thanks again.

Best, Rikki

I agree with @Mensur Dlakic keep trying to install your first alternatives. Send us the log of your failed attempts and we will try to help you. Installing programs is almost always a pain, which is why I strongly recommend you to use Conda (miniconda). Conda is really easy to set up and I think you can install all the programs you mentioned above with it in just one line of code in a virtual environment without sudo.

This is the miniconda page look for a tutorial on youtube if you need it, but basically just download the executable and then run its installation script.

By the way, I had good results with this tool, try it if you want: medusa. It can be run from a web browser or as a standalone tool (which you can easily install via conda).

Dear Mensur,

I eventually managed to install mummer4 and to generate a figure of the alignment between my reference "GCF_000006765.1_ASM676v1_genomic.fasta" and my contigs "pseudo_contig.fasta" using the following code as per the manual:

 ./mummer -mum -b -c GCF_000006765.1_ASM676v1_genomic.fasta pseudo_contig.fasta > mummer.mums
 mummerplot -postscript -p mummer mummer.mums

I was expecting a dotplot as shown in the manual, but instead the output is a graph more resembling a percent identity plot, except that it actually has the reference on the x-axis (and not percent identity) and query on the y-axis:

Does it seem like I have done something wrong, or is there a way to interpret this figure?

Best, Rikki