Cameron Gilchrist

Sorry for taking a while to get back to this. I can't confirm this issue, running clinker on my end with those two files produces:  The ``WARNING - Could...

How big are these genomes? The tool was designed for smaller gene clusters, and will struggle if you try to do full genomes - it aligns every protein from every...

A while back I added the `--ranges` argument where you can specify genomic coordinates to be extracted (e.g. `--ranges scaffold_1:10000-50000`). Though, some people were having issues with it (https://github.com/gamcil/clinker/issues/62) and...

Some good suggestions - sorry for being to late responding, been pretty busy lately with non clinker stuff :) As of v0.0.17 (just released), number 1 is implemented. Other points:...

Not currently, but a couple of people have asked for this so I'll try and add it to the next release.

Hi @azazelsan, sorry it took so long but I've added the ``-mo, --matrix_out`` argument in clinker v0.0.22 to do this. For instance, using the clusters in the ``examples`` folder of...

Hi @Yuki0902, The `--mo` parameter gives you the similarity scores between the input clusters (i.e. calculated from all gene alignments between two clusters). This is the matrix that is used...

Unfortunately I think you are both hitting some weirdness with how the genes get grouped and I don't have a good resolution for it. Currently they are computed by finding...

We handled this via email, but just for record keeping, this is caused by sequence features spanning the origin in circular sequence records. I implemented some functionality to try and...

Hi Olivier, is it possible to upload one of your input files so I can have a look?