Question: Phylogenetic diversity and Phylogenetic tree
0
gravatar for ashakoor
3.4 years ago by
ashakoor0
ashakoor0 wrote:

Hello, Is it possible to calculate Phylogenetic diversity with out constructing the tree? Other thing is that can we transform the number of reads into 1 0 (binary) data to calculate the phylogenetic diversity? I have never done such analysis before, so I am just curious to know. I do not have sequence data. I have only number of reads of fungi detected in plants. Looking forward to hear!! Best Regards, Abdul

fungi phylogenetic tree forum R • 1.2k views
ADD COMMENTlink modified 3.4 years ago by mks002190 • written 3.4 years ago by ashakoor0

Hello Michael I did not refer to alpha or beta diversity. I just want to simply calculate the Phylogenetic diversity. So tree is necessary to be built in order to calculate PD.

ADD REPLYlink written 3.4 years ago by ashakoor0
0
gravatar for Michael Dondrup
3.4 years ago by
Bergen, Norway
Michael Dondrup47k wrote:

Apart from phylogenetic diversity, there are different measures of ecological diversity such as alpha or beta diversity which can be computed from environmental 16sRNA samples using the OTU concept. Maybe you are referring to those?

Wrt to the definition of phylogenetic diversity on Wikipedia:

It is defined and calculated as "the sum of the lengths of all those branches that are members of the corresponding minimum spanning path",[1] in which 'branch' is a segment of a cladogram, and the minimum spanning path is the minimum distance between the two nodes.

If we accept this definition, then it does strictly require a cladogram, and I don't see how it could be computed without having one. If you mean, 'without constructing the tree _yourself_', you could use a precomputed tree.

ADD COMMENTlink modified 3.4 years ago • written 3.4 years ago by Michael Dondrup47k
0
gravatar for mks002
3.4 years ago by
mks002190
Bangalore. India
mks002190 wrote:

Hello Ashakoor,

U can check the link below and hope it would be some what useful.

http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0145364

ADD COMMENTlink written 3.4 years ago by mks002190
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