How To Draw Of Minimum Spanning Tree Of Sequences?

Question

[Joseph Hughes]

I would like to draw minimum spanning trees of a bunch of sequences. Some sequences are in multiple copies so I would like this to be represented as proportional circles. I am aware of the costly Bionumerics (Applied maths, Belgium) that does what I want see this but I want something free. I am also aware of mst in the ape library of R, spantree in the vegan library and minimum.spanning.tree in the igraph library but none of these let me specify the size of the circle according to number of sequence copies.

Answer 1

[jhc]

Joseph,

Take a look at the ETE library (Python and open source). You can write your own scripts to dynamically control the size and aspect of tree nodes according to any criteria.

Node/circle size can be changed very easily with ETE. You can find an example within my answer to this older post

hope it helps!

Answer 2

[Vitis]

Are you looking for haplotype networks based on parsimony? TCS might be the tool you need.

[Joseph Hughes]

I was looking for a distance based approach but thank you for the suggestion.

Answer 3

[Jacknathan]

Phyloviz might do it?

[Joseph Hughes]

This is exactly what I was looking for. Thanks.