<div dir="ltr">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<br><br>https://groups.google.com/forum/#!topic/bio-phylo/-tsR-GktiUQ<br><br>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.<br><br>Could anyone help me figure out how to get the correct branch length score in Perl?<br><br>On Monday, August 8, 2016 at 6:42:21 PM UTC-4, Fields, Christopher J wrote:<blockquote class="gmail_quote" style="margin: 0;margin-left: 0.8ex;border-left: 1px #ccc solid;padding-left: 1ex;">Cool, good to know.  Thanks for replying back here!
<br>
<br>chris
<br>
<br>> On Aug 8, 2016, at 3:19 PM, lskatz <<a href="javascript:" target="_blank" gdf-obfuscated-mailto="aHRP1ywJDQAJ" rel="nofollow" onmousedown="this.href='javascript:';return true;" onclick="this.href='javascript:';return true;">lsk...@gmail.com</a>> wrote:
<br>> 
<br>> A bioperl user directed me to Bio::Phylo which has the two functions that I
<br>> think I need:  calc_symdiff() and calc_branch_length_distance().
<br>> 
<br>> 
<br>> 
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