My ultimate aim is to make a plot which merges a heatmap and a phylogenetic tree. I have accomplished the heatmap and I have also found ETE2 package in BioPython which could help me merge the two kinds of plots, however ETE2 requires Newick format(tree like) rather than distance matrix (which I have) as input. Does anyone know of a module in BioPython to help me do this?
Conversion of distance matrix to Newick format
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It seems that in Biostars there is a thread about it. Which points to an answer to convert these formats and then following this discussion of the ETE mailing list.
I found this converter online, I am not sure if it works for you.
Asking to find a tool is offtopic, and I just made a google research...