Docs for different methods to annotate AA muts

[joverlee521]

We currently have two methods for annotating AA muts.

1. The traditional path explained in the Creating a pathogen workflow tutorial uses augur ancestral for NT muts and augur translate for AA muts.
2. The new feature to allow augur ancestral to reconstruct AA muts

We should have docs to compare the two method to annotate the AA muts with suggestions on when to use each method.
This should also point to existing repos as examples that use each method.

[jameshadfield]

This would be great. The major differences I see are that (1) has worse AA alignments due to gap placement, but the AAs are always 1-1 with the nucleotide mutations whereas (2) has better AA alignments but loses the relationship between nuc mutations and corresponding AA mutations, as shown in Auspice.

[jameshadfield]

Related Slack thread from a few months back