getnewickstr does not work on the output of getmatrix

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Alireza 2014-9-3

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关闭： MATLAB Answer Bot 2021-8-20

I have a tree as following,

tree_newick = '(A:4,(B:3,(C:1.2, D:1.5)F:1)E:2.5)O:0';
[dist_matrix, ID, DIST] = getmatrix(mytree);
getnewickstr(dist_matrix)

Error using seqlinkage (line 65) Size of DIST not compatible with the output of the SEQPDIST function.

I believe "getnewickstr", only function on pair-wise matrices. so the question is, is there any function to produce similarity matrix of a tree_newick_format data ?

Thanks

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Answer 1

Arthur Goldsipe 2014-9-5

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A quick search of the documentation for the term Newick shows that phytreeread will read files containing trees in the Newick format. This means you'll need to make sure the tree string is stored in a file somewhere.

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Answer 2

Alireza 2014-9-5

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Thanks for your reply.

The problem is not about reading the Newick - since I can read it and run the getmatrix on it. The problem is about calculating the dist_matrix.

As I explain, "I believe "getnewickstr", only function on pair-wise matrices. ". so the question is, is there any function to produce similarity matrix of a tree_newick_format data ?