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Question: Phylogenetic diversity and Phylogenetic tree
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gravatar for ashakoor
4.4 years ago by
ashakoor • 0
ashakoor • 0 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 • 1.4k views
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modified 4.4 years ago by mks002 • 190 • written 4.4 years ago by ashakoor • 0

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 REPLY • link written 4.4 years ago by ashakoor • 0
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gravatar for Michael Dondrup
4.4 years ago by
Michael Dondrup ♦ 48k
Bergen, Norway
Michael Dondrup ♦ 48k 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 COMMENT • link modified 4.4 years ago • written 4.4 years ago by Michael Dondrup ♦ 48k
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gravatar for mks002
4.4 years ago by
mks002 • 190
Bangalore. India
mks002 • 190 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 COMMENT • link written 4.4 years ago by mks002 • 190
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