Question: Phylogenetic tree with 0,1 matrix as the input?
0
gravatar for Shicheng Guo
11 months ago by
Shicheng Guo8.3k
Shicheng Guo8.3k wrote:

Hi All,

I want to build a tree to reflect the relationship between multiple samples with the following style (Figure 1a, Nature Genetics, PMID: 27749841). Suppose I have a 0,1 matrix, rather than DNA sequences/variants matrix, as the right panel of the phylogenetic tree, is there any method to build a similar figure? R or Python package is preferred. I am not sure whether mega 7 can show the tree like this style.

Thanks.

enter image description here

Phylogenetic trees were constructed from all somatic mutations by the Wagner parsimony method.

matrix phylogenetic • 585 views
ADD COMMENTlink modified 11 months ago by Sishuo Wang200 • written 11 months ago by Shicheng Guo8.3k
1
gravatar for Sishuo Wang
11 months ago by
Sishuo Wang200
The Chinese University of Hong Kong
Sishuo Wang200 wrote:

hi shicheng, i think both raxml and iq-tree can work with binary data.

ADD COMMENTlink written 11 months ago by Sishuo Wang200

Great. I will check these two tools. Thanks for the suggestion.

ADD REPLYlink written 11 months ago by Shicheng Guo8.3k
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