RAxML-NG 2 (dev version) questions

[Kenta Renard]

Dear All,

Very excited for the incoming RAxML-NG 2. I downloaded the current development version since I wanted to improve the phylogenies of the datasets I have.

I have done some substantial (lots of optimisation) amounts of work with RAxML-NG version 1 but I want to see if the new topology optimisation methods can improve my phylogenies.

If I start to perform new ML tree searches (and bootstrapping) with the current dev version, is it sufficiently close to the release version that I can simply cite the version2 paper? Would it be better to wait (in this case when do you expect Version 2 to be released?)

Best wishes,
Kenta 

[Oleksiy Kozlov]

Dear Kenta,

> Very excited for the incoming RAxML-NG 2. I downloaded the current development version since I
> wanted to improve the phylogenies of the datasets I have

great :)

> If I start to perform new ML tree searches (and bootstrapping) with the current dev version, is it
> sufficiently close to the release version that I can simply cite the version2 paper? Would it be
> better to wait (in this case when do you expect Version 2 to be released?)

We are currently evaluating a new adaptive search heuristic which, if adopted, could potentially
change the results. So I'd say it is a bit too early to use the dev version for production runs.
But please feel free to test it on your datasets and report the results/bugs :)

Our current plan is to release v2 beta in May/June, and final version by the end of 2025.

Best,
Oleksiy

[Anastasis Togkousidis]

Dear Kenta,

If you intend to publish any results inferred from the current adaptive heuristic in RAxML-NG v2.0 (dev), please include in your references the Adaptive RAxML-NG paper:

https://doi.org/10.1093/molbev/msad227

Evidently, you might switch to RAxML-NG v2.0 reference once it is released (and possibly published).

Best,
Anastasis