Phykit

- Added faidx (alias: get_entry; ge) function to extract fasta entries
from a multi-fasta file

- Added rooting procedure before calculating RF to handle comparing
unrooted and rooted trees

- function that calculates Robinson Foulds distance (robinson_foulds_distance;
rf_distance; rf_dist; rf) now can take trees that differ in topology. PhyKIT
will first determine shared tips between the two trees and prune both trees
to a common set of tips. Next, PhyKIT will calculate the Robinson Foulds
distance.

- Added function (column_score; cs) to calculate the quality of
an alignment given an input query alignment and a reference
alignment to compare it to

- Added function (sum_of_pairs_score; sops; sop) to calculate
the quality of an alignment given an input query alignment
and a reference alignment to compare it to

- PhyKIT now handles error stemming from piping output