dendrogram from precomputed distance matrix

I have looked around for an answer for this by have not been able to find one so I have come here. I have a precomputed distance matrix from an all vs all comparison of the root mean squared deviation (RMSD) of different protein structures.

         0    0.5770    0.4910    1.6840    0.6660    0.8970    1.0920    0.5380    0.6390    0.8100
    0.5770         0    0.6540    2.2020    0.2370    0.8790    0.9440    0.6120    0.4030    1.2530
    0.4910    0.6540         0    1.7360    0.6300    0.7520    1.4530    0.3460    0.4630    1.1190
    1.6840    2.2020    1.7360         0    2.2740    2.0790    2.5400    1.8480    2.1110    1.3380
    0.6660    0.2370    0.6300    2.2740         0    0.8560    1.0880    0.5900    0.3360    1.3490
    0.8970    0.8790    0.7520    2.0790    0.8560         0    1.4620    0.6840    0.7260    1.4480
    1.0920    0.9440    1.4530    2.5400    1.0880    1.4620         0    1.3330    1.2400    1.3950
    0.5380    0.6120    0.3460    1.8480    0.5900    0.6840    1.3330         0    0.3260    1.0900
    0.6390    0.4030    0.4630    2.1110    0.3360    0.7260    1.2400    0.3260         0    1.2800
    0.8100    1.2530    1.1190    1.3380    1.3490    1.4480    1.3950    1.0900    1.2800         0

I want to draw a dendrogram from this matrix:

tree=linkage(matrix,'average')
dengrogram(tree,0)

but if I do this the y-axis distance is all wrong because it's calculating the euclidean distances in the linkage. Is there a way to draw dendrograms directly from a precomputed distance matrix?

[KA]

Found the answer to my own question.

% for a symmetric matrix A

[rows columns] = size(A); v = []; for i = 1:rows-1 v = [v A(i,i+1:columns)]; end

Answer 1

[KA]

Found the answer elsewhere.

% for a symmetric matrix A

[rows columns] = size(A);
v = [];
    for i = 1:rows-1
                v = [v A(i,i+1:columns)];
    end

[Guillaume]

Note that a much simpler and faster way to obtain the same result would be:

v = A(tril(true(size(A)), -1))';

Answer 2

[crow white]

I would like to do the same: I have a precomputed distance matrix (calculated on data using the bray-curtis index) and I want to draw a dendogram of the results. I don't see how your solution draws the dendrogram. Thanks for your help

[KA]

I don't know if your problem is the same as mine. The problem I had was clustering and all-v-all distance matrix because you cannot calculate euclidean distances directly from these data in matlab. However, it is possible if you first convert the distance matrix to a linkage vector and then prepare a dendrogram from this vector using standard matlab commands. the script for converting the distance matrix to a vector is below output v_mat - good luck.

% for a symmetric matrix 'name'

 [rows,columns] = size(matrix);
 v_mat = [];
    for i = 1:rows-1
                v_mat = [v_mat matrix(i,i+1:columns)];
    end