Similarity score and plotting

[LemoAlex]

Hi clinker users,

I am running into some issues with the program, and I don't really understand why / how this is happening. The program seems to be mishandling some genes that should be showing some similarity. (or something that I do not understand is happening). The general clustering and alignment works fine but some details in some genomes are indeed weird.

For instance :

In this example, B and C are almost clonal sequences, so I don't understand why the purple arrow is not also shown in C. I checked the fasta alignment, and sequences are almost identical.

Also. the "red/pinkish" arrow present in A should also be recognized in B and C, as they share some high similarity when looking at the fasta file ( > 90 %).

Any idea of what is happening?

I am using .gbk files as input (with specified ranges) and I am running clinker v0.0.25 on a virtual environment through conda.

Thank you for your help, Best,

Alexandre

[gamcil]

Hi Alexandre, is it possible to upload your files so I can take a look? I'm not sure exactly what's causing it, but my guess would be something to do with how clinker is reading them in.