Leighton Pritchard

The changes have now been pulled into [`pr_236`](https://github.com/widdowquinn/pyani/tree/pr_236) to be brought in line with existing tests, CLI expectations, and for further development. @all-contributors please add @TSL-RamKrishna for code, ideas

It is still in progress. The current status is that the `pr_236` branch will run on SLURM. However, we need to refactor how we aggregate jobs within `pyani` because SLURM...

Aye - I need to make progress on this for my own stuff, but this time of year is unpleasantly busy.

This is a filesystem issue also. Writing thousands to millions of small files to the filesystem degrades performance. They are also painfully slow to delete. A process of: - call...

Using `pip` instead of `conda` should work fine. I think it's OK to have a single set of instructions across all platforms recommending `pip` for `biopython`, `bioservices` and `seaborn` (for...

Re: terminals Anaconda Prompt gives access to all the `conda` executables, but behaves as a Windows CMD prompt (no `ls` or other Bash commands). Git Bash gives us `git` (which...

Yes - Jalview attempts to do a 'nice' job on Windows, but on Windows 10 the installer fails. Happily the `.jnlp` webstart works for Jalview. Artemis is straightforward in that...

Hi @artfet - you'll need the `--force` option as well, as in the example from @peterjc - `pyani/average_nucleotide_identity.py -i . -o demo --graphics --skip_nucmer --force --noclobber` You might want to...

> My understanding of the issue is that regardless of the order in which the genomes are processed, we should obtain the same values for aligned bases. My initial thoughts...

> I think `nucmer` is not symmetrical, at least not in practice. That may be true, but I would be interested to know whether the IntervalTree count of aligned bases...