Trees contain a single taxa at a node

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Michael Sennett

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Nov 15, 2019, 2:25:06 PM11/15/19
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Hello,

I am using bali-phy v3.4.1.

Command line: 

( nice bali-phy --align ${FILE} --alphabet Amino-Acids --smodel lg08+f+Rates.gamma --imodel rs07 --iterations=100000000 & > ${FILE%.*}.log ) &


We have run this three times, with different sets of sequences, and keep getting a single taxa at a node, rather than a leaf.


I have attached the MAP tree that was exported when we analyzed our results. ABH_ALBA is the taxa that appears at the node when we visualize the trees using FigTree. It is other sequences when we modify the sequence set. The alignment seems to be incorporating the sequences fine. 


Thanks for your help in advance.

Mike

MAP.tree

Benjamin Redelings

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Nov 15, 2019, 9:25:07 PM11/15/19
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Hi Michael,

Thanks for the bug report!

1.  Just to make sure I'm understanding you correctly, are you concerned about the root node being a named tip? For example,

((a:1.0,b:2.0):3.0)c;

versus

(a:1.0,b:2.0,c:3.0);

Technically these are both legal Newick format, but I think people generally expect the second one.  And figtree only does not seem to handle it correctly [1].

2. If you look at the file MAP.tree, you can see it ends with

...........................):0.000129269133362):0.000302274136706)'ABH_ALBA';

3. I believe this bug is fixed in bali-phy on github.  Can you compile and install the github version, or would that be too complex?

If you can install bali-phy from there, then you should be able to rerun bp-analyze on your old output without rerunning the chains.

-BenR

[1] Note that if you enable "Node Labels" in Figtree and select the last option (usually "label") then the missing name shows up in Figtree, but not quite in the right spot.

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