MATLAB: Is it possible to seqlinkage with a maximum parsimony or minimum evolution method

Question

I try do construct a phylogenetic tree on basis of maximum parsimony (minimum evolution). The function seqlinkage can do this. Method choices are only UPGMA, single-linkage and others, but not the most basic: maximum parsimony. Is there another way to archieve this?

Answer 1

Dear Anton Huegel,

I am not really familiar with constructing phylogenetic trees in MATLAB, but I believe you could use the function seqneighjoin.

MATLAB's example on phyltrees using hominid data states that:

"A neighbor-joining tree can be built using the seqneighjoin function. Neighbor-joining trees use the pairwise distance calculated above [in the example] to construct the tree. This method performs clustering using the minimum evolution method."

So this seems to indicate that the minimum evolution method is in fact included in MATLAB's bioinformatics toolbox...

If this is not sufficient for you: It also seems there is another toolbox available (see also file exchange) made by Cai and co-workers called MBEToolbox, which focuses on sequence data analysis. I had a quick look at it and it seems that maximum parsimony is available there.

Edit: some more on Cai's MBEToolbox: here