Bernhard Haubold

Could you please post a sample of the offending file(s)? Thanks, Bernhard.

Thanks, I downloaded the four assemblies you list and constructed a tree from them using [phylonium](https://github.com/evolbioinf/phylonium) and three programs from my [biobox](https://github.com/evolbioinf/biobox): `$ phylonium *.fna | nj | midRoot |...

Did you unzip the data under Windows or Mac? These operating systems use other newline characters than Unix, which might then confuse macle. If that were the case, you could...

Thanks for pointing this out, there was an error in the version checking of fur. I've fixed this now and also pushed the repaired docker container.

In your analysis there is no output from the sliding window step. So the next step fails. It should perhaps fail more gracefully, but there we are.

Thank you for pointing out this problem. The solution is to also install the program `plotLine`, which is part of the [biobox](https://github.com/evolbioinf/biobox) repository. I have now clarified the dependency on...

To a first approximation, each neighbor sequence is turned into a suffix array. Since the computation of a suffix array comes with a performance overhead, the analysis of very many...

Thank you for pointing out this error. The package `libdivsufsort-dev` was missing from the list of dependencies. This package calculates the suffix array underlying `fur`. I have now added `libdivsufsort-dev`...

Thanks for pointing out these additional dependencies. I've added just them to the `README`, too.

The -r switch in makeFurDb takes as argument the name of the file containing the target representative. Without -r, makeFurDb uses the longest target as representative. Does that help?