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llrs
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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.

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 ade4ade4 and Bioconductor package made4made4

Also have a look at the phylogenetic R package adephyloadephylo and several related packages https://cran.r-project.org/web/packages/adephylo/index.html

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 https://cran.r-project.org/web/packages/adephylo/index.html

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

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Aedin
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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 https://cran.r-project.org/web/packages/adephylo/index.html