Treedist

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Treedist

lskatz
Hi, I am wondering if Phylip's treedist or the actual Robinson-Foulds and Kuhner-Felsenstein algorithms are implemented anywhere.  If not, is anyone thinking of doing it?  I would try it myself but I am not sure if I would get it done correctly without help.
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Re: Treedist

lskatz
A bioperl user directed me to Bio::Phylo which has the two functions that I think I need:  calc_symdiff() and calc_branch_length_distance().
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Re: Treedist

Fields, Christopher J
Cool, good to know.  Thanks for replying back here!

chris

> On Aug 8, 2016, at 3:19 PM, lskatz <[hidden email]> wrote:
>
> A bioperl user directed me to Bio::Phylo which has the two functions that I
> think I need:  calc_symdiff() and calc_branch_length_distance().
>
>
>
> --
> View this message in context: http://bioperl.996286.n3.nabble.com/Treedist-tp17915p17916.html
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Re: Treedist

lskatz
Hopefully you all can forgive me about posting about Bio::Phylo here but I am not getting much help over there.  I posted this on their site

https://groups.google.com/forum/#!topic/bio-phylo/-tsR-GktiUQ

I have figured out Robinson-Foulds (symmetric difference), so we can move on from that.  However, I have not figured out how to run the branch length distance correctly yet such that it matches the Phylip treedist program.  The Bio::Phylo code looks correct but I believe, given its legacy and expertise behind it, that treedist must be right.  I also confirmed the value in the R phangorn package using treedist(), and it agrees with Phylip.

Could anyone help me figure out how to get the correct branch length score in Perl?

On Monday, August 8, 2016 at 6:42:21 PM UTC-4, Fields, Christopher J wrote:
Cool, good to know.  Thanks for replying back here!

chris

> On Aug 8, 2016, at 3:19 PM, lskatz <<a href="javascript:" target="_blank" gdf-obfuscated-mailto="aHRP1ywJDQAJ" rel="nofollow" onmousedown="this.href=&#39;javascript:&#39;;return true;" onclick="this.href=&#39;javascript:&#39;;return true;">lsk...@...> wrote:
>
> A bioperl user directed me to Bio::Phylo which has the two functions that I
> think I need:  calc_symdiff() and calc_branch_length_distance().
>
>
>
> --
> View this message in context: <a href="http://bioperl.996286.n3.nabble.com/Treedist-tp17915p17916.html" target="_blank" rel="nofollow" onmousedown="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fbioperl.996286.n3.nabble.com%2FTreedist-tp17915p17916.html\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNHHKz_Nc8mtIpIqTS_jCKwWFKCfdg&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fbioperl.996286.n3.nabble.com%2FTreedist-tp17915p17916.html\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNHHKz_Nc8mtIpIqTS_jCKwWFKCfdg&#39;;return true;">http://bioperl.996286.n3.nabble.com/Treedist-tp17915p17916.html
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