Using multidimensional scaling to visualize protein sequences by functionality
Some of the first MSA analysis, eg of codon usage of bacteria were performed using matrix factorization (see old papers from Des Higgins). His group also published discriminative methods for finding functional residues using supervised correspondence analysis 


  Wallace IM1, Higgins DG BMC Bioinformatics. 2007 Apr 23;8:135.
  Supervised multivariate analysis of sequence groups to identify
  specificity determining residues.


The method is available in the R package ade4 and Bioconductor package made4

Also have a look at the phylogenetic R package adephylo and several related packages