fixes #16

[the-mayer]

Description

The latest version of the phangorn package no longer exports read.aa(), a function MolEvolvR utilized. The functionality of read.aa() has been present in read.phyDat() for some time, using the type = "AA" argument. This PR updates MolEvolvR to use read.phyDat() and fixes #16

What kind of change(s) are included?

• Feature (adds or updates new capabilities)
• Bug fix (fixes an issue).
• Enhancement (adds functionality).
• Breaking change (these changes would cause existing functionality to not work as expected).

Checklist

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[epbrenner]

Looks good. In reviewing some of the surrounding code, a lot of it is outdated, redundant, and in need of a refactor, but I'm putting that on my to-do list. We should be good to merge as-is since most of that outdated code isn't actively used.

[the-mayer]

Thanks @epbrenner for the review and the additional attention to these functions! Merging for now to get pkgdown builds back up and running 👍