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
+\ No newline at end of file