Question: Where To Get A Mammalian Phylogenetic Tree With Branch Distances.
2
gravatar for Biojl
7.7 years ago by
Biojl1.7k
Barcelona
Biojl1.7k wrote:

Hi,

Anyone knows a place to download an updated version of the reconciled mammalian phylogenetic tree with branch distances? Ideally in newick format.

I currently use the data from this paper: http://genome.cshlp.org/content/17/12/1797.full?sid=439dbed9-fbcb-402d-abca-55a5ed0db230

But I have to extract the info manually from there and re-calculate the distances for a few species.

Thanks!

phylogenetics tree • 6.4k views
ADD COMMENTlink written 7.7 years ago by Biojl1.7k
9
gravatar for a.zielezinski
7.7 years ago by
a.zielezinski9.2k
a.zielezinski9.2k wrote:

I always use TimeTree, a public resource for knowledge on the timescale and evolutionary history of life.

See on youtube how it works: Kelly explains TimeTree.

ADD COMMENTlink modified 7.7 years ago • written 7.7 years ago by a.zielezinski9.2k

this is really cool!

ADD REPLYlink written 7.7 years ago by Whetting1.5k

Very cool indeed! They even have an app for mobiles! Awesome :)

ADD REPLYlink written 7.7 years ago by Biojl1.7k
5
gravatar for Josh Herr
7.7 years ago by
Josh Herr5.7k
University of Nebraska
Josh Herr5.7k wrote:

In Webb Miller et al's paper, the paper you cite, there is a link to an alignment file, and the data set is also on Galaxy. You can create a newick file (Mammalian examples here) from one of many phylogenetic programs out there: I prefer both RAxML for maximum likelihood based methods (github here) and MrBayes (sourceforge here) for Bayesian analysis. Quick and easy to get a tree with branch lengths from their dataset. I like viewing trees in FigTree.

I searched for a few minutes on Google and didn't find any newick files that were readily available that matched exactly what you want, but that's not to say that they are not out there. You should be able to draw a phylogenetic tree from the dataset they provide in less time than it would take you to search the web for a close approximation and then modify it to match this paper.

If you're really challenged by all of that and can't reproduce their branch lengths for some reason or another and you want to exactly reproduce the phylogenetic tree with branch lengths they show in the supplemental data, then, ultimately, you can use TreeSnatcher to write a newick file from an image.

ADD COMMENTlink written 7.7 years ago by Josh Herr5.7k

Hi Josh, I'm willing to use some species that have been sequenced since the publication of that paper, that's why I'm asking for an updated version. Anyway your approach is very useful, thanks!

ADD REPLYlink written 7.7 years ago by Biojl1.7k
1
gravatar for Biojl
7.7 years ago by
Biojl1.7k
Barcelona
Biojl1.7k wrote:

I already made a matrix with the data extracted from TimeTree. I've found that there are a lot of discrepances with data coming from there and data coming from onezoom.

For instance the divergence time between megabat (Pteropus vampyrus) and microbat (Myotis lucifugus) is 57.5 Million years for timetree.org abd 71.2 Million years in onezoom.org

ADD COMMENTlink modified 7.7 years ago • written 7.7 years ago by Biojl1.7k

Yes, but you have to remember that phylogenies are only hypotheses and measuring divergent time is an estimate. The only way you can be sure is to build a time machine. I wouldn't stress out that divergent times match up, but be prepared to explain why.

ADD REPLYlink written 7.7 years ago by Josh Herr5.7k

I didn't know they different approaches could be that different. Anyway thanks again, you've opened me a full world of possibilites!

ADD REPLYlink written 7.7 years ago by Biojl1.7k

TimeTree cannot be parsed anymore in a semi-automatic way... damn it.

ADD REPLYlink written 6.0 years ago by Biojl1.7k
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