james hadfield

This has been fixed (quite some time ago) so I don't think it's a bug. That being said, it would be nice to check the output against a known pdf...

Hi Valery, the y-axis is the number of recombination events observed which cover that particular position in the genome. Note that an event may involve many strains but only be...

> Do you mean exactly the number of strains that were detected in the regions of recombination on that position? No, the number of recombination events. If a recombination event...

This exists in phylocanvas. @simonrharris perhaps you could ask @richardgoater about how to do this.

Hi @cirodri1! > Is there a way to root the phylogenetic tree at a specific branch in Phandango? Not currently. One solution would be to use a unix-y tool for...

I'm not familiar with scoary files, but phandango can handle plink (and plink-like) formats (see https://github.com/jameshadfield/phandango/wiki/Input%20data%20formats#manhattan-plots) so if it's possible to convert into this format you _should_ be able to...

already done 8ecb87f

how does a moused-over block go off the screen when you're zooming? I can't recreate this

Not currently - although we used to show a grey column under the gene (where the recombination blocks are) when a gene was highlighted / selected. Would this be of...

I'm not sure I completely understand - could you post a screenshot? thanks