Question: about Phylogenetic tree and divergence time
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gravatar for porori3000
3.4 years ago by
porori30000
porori30000 wrote:

First of all, I'm a student in non-English-speaking country... Newbie in bioinformatics. My Question is about Phylogenetic tree and divergence time. (for training) For drawing Phylogenetic tree, I used MEGA 7 for windows 7 64bit, GUI.

I draw the tree with 16 species mtDNA .fasta data and new mtDNA data, and then I try to calculate the divergence time. But I don't know how to calculate this time. So... the first question is 'Is it possible to calculate divergence time with MEGA7? if possible, how? And if it is impossible or not recommendable, what tools can be used for it?'

Anyway in this situation I did something with MEGA7. (maybe... pointless task?) I found "Compute Pairwise distance..." and get a matrix from it. But I don't know what these numbers mean. 0.05731, 1.012493, 1.42815, 1.197099 .... no unit. Surely this values looks like getting bigger if compared two species have distant evolutionary relationship. What is it? It is my second question. If you have an idea for at least one of these questions, please comment and help me... thanks.

ADD COMMENTlink modified 3.4 years ago by Michael Dondrup46k • written 3.4 years ago by porori30000
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gravatar for Michael Dondrup
3.4 years ago by
Bergen, Norway
Michael Dondrup46k wrote:

To compute divergence time requires calibration data for some taxa. Simply speaking, the calibration allows for an estimate of the correspondence between the number of substitutions/mutations and years since divergence (Say: "In this branch we expect to see 10 mutations per 1kb per 1000 years", this is totally made up figures and oversimplified but I hope you get my point). You can get expert estimates of divergence from TimeTree.

ADD COMMENTlink modified 3.4 years ago • written 3.4 years ago by Michael Dondrup46k
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