Those are R-codes for the direct PCA to sequences: both for nucleotides and amino acids.
The sequences are transformed into boolean vectors, forming a matrix. The matrix is decomposed into a set of singular matrixes, from which the principal components are found. The processes are rather simple; I hope the codes are readable ones.
I usually write the codes all alone. Hence I am not familiar with the ecosystem of Git, and at present, I am not sure whether or not I will maintain the altered versions in the future. However, please feel free to ask me any questions via e-mails.
Tomokazu Konishi konishi@akita-pu.ac.jp