Update ViralMSA

[niemasd]

Earlier today, I fixed a bug in ViralMSA in which consensus sequences with long stretches of NNNN...NNNN sometimes would get truncated (I think when stretch length was greater than ~300), and I incorporated the fix into ViralMSA 1.1.12. I don't think we should ever be encountering this bug given that we are only performing phylogenetic inference on high-quality consensus sequences (so we shouldn't have long stretches of NNN...), but it would be good to update just in case

Note that ViralMSA can be updated as follows (assuming ViralMSA.py is in your PATH):

ViralMSA.py -u

EDIT (2021-04-14): I just rolled out ViralMSA 1.1.13. The new feature implemented in this version is not relevant to our analysis, but just wanted to update my GitHub Issue accordingly (ViralMSA.py -u will update to 1.1.13)

[niemasd]

I've made a couple more updates to ViralMSA since then, so I'll keep the version number in the issue generic. No major changes have been made, so whenever we get around to it, we can update to the newest version