Question: Phylogenetic tree with 0,1 matrix as the input?
0
gravatar for Shicheng Guo
7 weeks ago by
Shicheng Guo7.8k
Shicheng Guo7.8k 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 • 172 views
ADD COMMENTlink modified 7 weeks ago by Sishuo Wang180 • written 7 weeks ago by Shicheng Guo7.8k
1
gravatar for Sishuo Wang
7 weeks ago by
Sishuo Wang180
The Chinese University of Hong Kong
Sishuo Wang180 wrote:

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

ADD COMMENTlink written 7 weeks ago by Sishuo Wang180

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

ADD REPLYlink written 7 weeks ago by Shicheng Guo7.8k
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