Phykit

- Added function to estimate site-wise evolutionary rate in an alignment. See function evolutionary_rate_per_site.

- Added function to recode alignments based on 8 different recoding schemes (7 for amino acids;
1 for nucleotides). See function recode

- Added an optional argument to the thread_dna function. Now, PhyKIT can thread nucleotide
sequences onto a trimmed amino acid alignment. To do so, point PhyKIT to the ClipKIT outputted log
file using the -c argument. The ClipKIT log file can be generated when trimming an alignment with
ClipKIT by adding the -l argument (see here for more details: https://jlsteenwyk.com/ClipKIT/).

-relative composition variability is now adapted for calculating compositional biases in
individual taxa. The new function in rcvt (relative composition variability, taxon).

- calculations of pairwise identity in alignment now supports excluding pairwise
combinations with gaps.

- hidden paralogy check now simply looks for monophyly or lack thereof for a set of taxa. Hidden paralogy
check still reports insufficient taxon representation.