Class A beta lactamases

Get a protein FASTA file of 1041 class A beta-lactamase alleles:

cp $TT/phylogeny/data/bla-A.fa.gz .
gunzip bla-A.fa.gz

Compute complete matrix of pairwise dissimilarities and store them in a Data master format file bla-A.dm:

$TT/dissim/fasta2dissim  -aa  -global  -blosum62  -power 0.5  -dataset bla-A  bla-A.fa
# Time: 10 min.

Make a tree:

$TT/phylogeny/makeDistTree  -data bla-A  -dissim_attr "dissim" \
  -variance pow  -variance_power 2  -optimize  -subgraph_iter_max 5 \
  -output_tree bla-A.tree
# Time: 8 min.

Use the same dissimilarities to compute multi-dimensional sclaling:

$TT/dm/mds  bla-A  -attr "dissim"  -attrType 1  -maxClusters 6  > bla-A.mds