save intermediate tree / locally optimal tree

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shenxing...@gmail.com

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Jul 30, 2021, 6:05:51 AMJul 30
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Hello,

I am quite interested in intermediate tree / locally optimal tree/ current-best tree during tree search. I saw the option “”-j” in raxml 8 that can save them. Is it possible that raxml-ng v 1.0 has this function too. Alternatively, how could I  modify the code in the  Checkpoint.cpp file?

Thanks a lot.

Xing

Alexey Kozlov

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Aug 2, 2021, 8:59:07 AMAug 2
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Hi Xing.

raxml-ng will store current-best tree into PREFIX.raxml.lastTree.TMP file, however this file will be
constantly overwritten and eventually removed upon successful search completion. If you want to save
all intermediate trees, you can modify the code here:

https://github.com/amkozlov/raxml-ng/blob/master/src/Checkpoint.cpp#L72

Best,
Alexey
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