FBP Support > 1

[mattjones315]

Hello,

First off, thank you so much for this brilliant work & software! I've found it very useful for assessing supports on my trees.

I did run into a slight issue, I believe, with some of the results from the FBP mode though. For the output I'm attaching, I'm finding FBP supports greater than 1:

((1_2012210001:1.000000,3_2012210001:1.000000)0.000000:1.000000,(4_2212210001:1.000000,2_2112210001:1.000000)1.500000:1.000000);

My understanding is that the FBP should be [0, 1] always, but is this necessarily the case? And if it is the case, why could I be getting supports > 1?

I'm attaching the trees I used as input, and I've run the program as so from command line:

./booster -i test_ref.txt -b test_boot.txt -o test_fbp.txt -a fbp

Thank you in advance!

Best, Matt

test_ref.txt test_boot.txt

[fredericlemoine]

Hello,

Thank you for your comment. I could check with your trees, and it seems that these are rooted trees (and in test_boot.txt it is a mix of rooted an unrooted trees). I corrected the computation, could you please tell me if it works with your trees now? Thank you,

Frederic

[mattjones315]

Fantastic, thank you!

Is the new code on github? If so, I'll repull and verify that it works. Thanks again!

• Matt

On Fri, May 22, 2020 at 2:06 PM fredericlemoine notifications@github.com wrote:

Hello,

Thank you for your comment. I could check with your trees, and it seems that these are rooted trees (and in test_boot.txt it is a mix of rooted an unrooted trees). I corrected the computation, could you please tell me if it works with your trees now? Thank you,

Frederic

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/evolbioinfo/booster/issues/6#issuecomment-632908657, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACKWFHR5KIHYS3AGEVXEDJTRS3SLTANCNFSM4NIB63MA .

[fredericlemoine]

It is on github, you can pull the last changes

Frederic

[mattjones315]

Great, thanks!

I have just repulled the code and upon trying to re-run the code, I encountered a segmentation fault. It appears to happen on the 6th tree:

---

• Options *

  ---

  booster : version v0.1.2-3-g91fb005a13 Input Tree : test_ref.nwk Bootstrap Trees : test_boot.nwk Output tree : test_fbp.txt Stat file : None Algo : fbp Count tax move/branch: false Threads : 1 Dist cutoff : 0.300000 Quiet : false

  ---

  Num trees: 8 New bootstrap tree : 0 New bootstrap tree : 1 New bootstrap tree : 2 New bootstrap tree : 3 New bootstrap tree : 4 New bootstrap tree : 5 Segmentation fault (core dumped)

Do you have any thoughts on why this might be happening? Did you say that with your changes you were able to compute the FBP correctly on these inputs?

Thanks again!

-Matt

[fredericlemoine]

Sorry, it should work now

[mattjones315]

Fantastic, it works now! Thanks so much. I'll close the issue now.