9 files changed, 1240 insertions, 0 deletions

diff --git a/test/entropy/GenomeAlignments.m b/test/entropy/GenomeAlignments.m
new file mode 100644
index 0000000..be56570
--- a/dev/null
+++ b/test/entropy/GenomeAlignments.m
@@ -0,0 +1,31 @@
+function [ALIGN inds] = GenomeAlignments(IN_GENOMES, DIST_MAT)

+%   GenomeAlignments

+%       This will align all of the protein segments in the genome structure

+%       and return a cell-array.  Each cell is the alignment of one

+%       protein.  If the protein is missing then the distance is NaN.

+%

+

+[tree inds] = MakeTree(DIST_MAT);

+ALIGN = malign(tree, inds);

+

+    function align=malign(tree, inds)

+        seqs = arrayfun(@(x)(x.Sequence), IN_GENOMES(inds), 'uniformoutput', false);

+        align = multialign(seqs, tree);

+    end

+

+

+

+    function [tree_obj inds]=MakeTree(dist_mat)

+        %   MakeTree

+        %       Takes a distance matrix and returns a tree object and the indicies

+        %       to the rows that are in the tree.

+        %

+        

+        inds = find(~all(isnan(dist_mat)|isinf(dist_mat)|dist_mat==0));

+        dvec = squareform(dist_mat(inds, inds));

+        dvec(dvec <= 0) = rand(nnz(dvec <= 0),1)*min(dvec(dvec>0));

+        tree_obj = seqlinkage(dvec);

+        

+    end

+

+end
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