Lucas Czech

For anyone in the future trying to find the FTP URLs for these cache datasets, try http://uswest.ensembl.org/info/docs/tools/vep/script/vep_download.html#installer and http://uswest.ensembl.org/info/docs/tools/vep/script/vep_cache.html#cache :-) There are links hidden under "Manually downloading caches" :-)

Agreed, that seems like a useful addition. On that note, it might also be good to specify numpy and pandas explicitly wherever relevant. I've had a lot of trouble with...

This seems to be solved in [issue 288](https://github.com/snakemake/snakemake-wrappers/issues/288) and [PR 300](https://github.com/snakemake/snakemake-wrappers/pull/300).

Probably, this should also include other comparison operators as well: `=`?!

Hi David, you are right with your human and gorilla example: for identical sequences, zero branch lengths of course make sense, and placing additional sequences on those branches doesn't, but...

The same is true for manually rooting the tree. Saving a re-rooted tree and then opening it again shows the original tree again. The nexus file contains: ``` set trees.rooting=true;...

I am also facing this issue. It does not only happen when opening files, but also when saving. It's not always reproducible, more like with a 1/3 probability.

Not sure if this is the reason for the crash, but I just got ``` java: ../../src/XlibInt.c:245: _XPrivSyncFunction: Assertion `dpy->synchandler == _XPrivSyncFunction' failed. ``` before a crash. Might help debugging.

Since a while (couple of weeks maybe), atom sometimes crashes immediately after startup, before showing the UI, with the following message:  It dumps its core, so I did some...

Same here... :-(