RAxML-NG v0.9 and Bioinformatics application note

[Alexey Kozlov]

Dear RAxML/RAxML-NG users,

yesterday we released RAxML-NG v0.9.0, which is the first RAxML-NG
version without a "BETA" tag:

https://github.com/amkozlov/raxml-ng/releases/tag/0.9.0

After more than two years of testing and bugfixing - and thanks to your
valuable feedback in this group! - we now consider RAxML-NG to be stable
enough for production analyses. Hence, we strongly recommend all
RAxML8.x users to upgrade (with the exceptions listed below)!

Documentation: https://github.com/amkozlov/raxml-ng/wiki
Short intro & lab: https://cme.h-its.org/exelixis/pubs/Krumlov2019_RAxML.pdf
Hands-on tutorial: https://github.com/amkozlov/raxml-ng/wiki/Tutorial

Furthermore, RAxML-NG application note has been recently accepted in
Bioinformatics, so please update your citations accordingly:

https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btz305/5487384

So why is it v0.9 and not v1.0? There are still a couple of commonly
used RAxML8,x features which are not yet available in RAxML-NG:

1. Rapid bootstrapping ("-x" option, also used in "-f a")

2. Coarse-grain parallelization across starting trees and bootstrap
replicates (RAxML-MPI/RAxML-HYBRID)

3. GTRCAT model (per-site rates, "Stamatakis-CAT")

The current plan for these features is as follows:

- RAxML-NG v1.0 (late June/July) will include rapid bootstrapping and
coarse-grained paralellization

- RAxML-NG v1.x (fall 2019) will include GTRCAT replacement (most
probably, something similar to IQTree's PMSF model)


Best regards,
Alexey

[Conor Meehan]

Hi Alexey,

I don't know if I have something wrong but the linux prepacked version appears to still be 0.8.1. The mac one was fine though...

Cheers,

Conor

[Alexey Kozlov]

oops my bad :(

It is fixed now, many thanks for spotting this, Conor!

Alexey

On 22.05.19 14:26, Conor Meehan wrote:
> Hi Alexey,
>
> I don't know if I have something wrong but the linux prepacked version appears to still be 0.8.1.
> The mac one was fine though...
>
> Cheers,
> Conor
>
> On Tuesday, 21 May 2019 17:45:46 UTC+2, Alexey Kozlov wrote:
>
> Dear RAxML/RAxML-NG users,
>
> yesterday we released RAxML-NG v0.9.0, which is the first RAxML-NG
> version without a "BETA" tag:
>
> https://github.com/amkozlov/raxml-ng/releases/tag/0.9.0
> <https://github.com/amkozlov/raxml-ng/releases/tag/0.9.0>
>
> After more than two years of testing and bugfixing - and thanks to your
> valuable feedback in this group! - we now consider RAxML-NG to be stable
> enough for production analyses. Hence, we strongly recommend all
> RAxML8.x users to upgrade (with the exceptions listed below)!
>
> Documentation: https://github.com/amkozlov/raxml-ng/wiki
> <https://github.com/amkozlov/raxml-ng/wiki>
> Short intro & lab: https://cme.h-its.org/exelixis/pubs/Krumlov2019_RAxML.pdf
> <https://cme.h-its.org/exelixis/pubs/Krumlov2019_RAxML.pdf>
> Hands-on tutorial: https://github.com/amkozlov/raxml-ng/wiki/Tutorial
> <https://github.com/amkozlov/raxml-ng/wiki/Tutorial>
>
> Furthermore, RAxML-NG application note has been recently accepted in
> Bioinformatics, so please update your citations accordingly:
>

> https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btz305/5487384 <https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btz305/5487384>

>
>
> So why is it v0.9 and not v1.0? There are still a couple of commonly
> used RAxML8,x features which are not yet available in RAxML-NG:
>
> 1. Rapid bootstrapping ("-x" option, also used in "-f a")
>
> 2. Coarse-grain parallelization across starting trees and bootstrap
> replicates (RAxML-MPI/RAxML-HYBRID)
>
> 3. GTRCAT model (per-site rates, "Stamatakis-CAT")
>
> The current plan for these features is as follows:
>
> - RAxML-NG v1.0 (late June/July) will include rapid bootstrapping and
> coarse-grained paralellization
>
> - RAxML-NG v1.x (fall 2019) will include GTRCAT replacement (most
> probably, something similar to IQTree's PMSF model)
>
>
> Best regards,
> Alexey
>

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[Wayne Pfeiffer]

Hi Alexey,

After I downloaded

  raxml-ng_v0.9.0_linux_x86_64_MPI.zip

and tried to compile, I got lots of errors such as the following:

[  1%] Building CXX object src/CMakeFiles/raxml_module.dir/._AncestralStates.cpp.o

/home/pfeiffer/comet/raxml-ng-0.9.0/src/._AncestralStates.cpp:1:1: warning: null character(s) ignored

     Mac OS X                2   ?      ?                                      ATTR       ?   ?   <                  ?   <  com.apple.quarantine q/0083;5ce5acaf;Safari;3738C532-776E-461C-9DF4-3EDC2E688FEB

* Could it be that the Mac OS source is being downloaded instead of the Linux source?

Best regards,  Wayne

[Alexey Kozlov]

Hi Wayne,

this is very weird, source files are identical for Mac and Linux...

What compiler version are you using?
Are you trying to compile MPI version on Mac? (I guess I never tried it)
Does src/AncestralStates.cpp file look normal? (broken archive?)

Best,
Alexey

On 23.05.19 01:33, Wayne Pfeiffer wrote:
> Hi Alexey,
>
> After I downloaded
>
> raxml-ng_v0.9.0_linux_x86_64_MPI.zip

> <https://github.com/amkozlov/raxml-ng/releases/download/0.9.0/raxml-ng_v0.9.0_linux_x86_64_MPI.zip>

> https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btz305/5487384 <https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btz305/5487384>

>
>
> So why is it v0.9 and not v1.0? There are still a couple of commonly
> used RAxML8,x features which are not yet available in RAxML-NG:
>
> 1. Rapid bootstrapping ("-x" option, also used in "-f a")
>
> 2. Coarse-grain parallelization across starting trees and bootstrap
> replicates (RAxML-MPI/RAxML-HYBRID)
>
> 3. GTRCAT model (per-site rates, "Stamatakis-CAT")
>
> The current plan for these features is as follows:
>
> - RAxML-NG v1.0 (late June/July) will include rapid bootstrapping and
> coarse-grained paralellization
>
> - RAxML-NG v1.x (fall 2019) will include GTRCAT replacement (most
> probably, something similar to IQTree's PMSF model)
>
>
> Best regards,
> Alexey
>

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[Wayne Pfeiffer]

Hi Alexey,

There must have been some problem with the files that I downloaded, since when I tried again, I was able to compile OK :) I still have been unable to get the executable to link to libpll, but I will work with someone here on that.

In answer to your first two questions, I have compiled with both gcc 7.2.0 and intel 2016.3.210 on our Comet supercomputer, which has Intel Haswell cores.

Best regards,  Wayne

On Wednesday, May 22, 2019 at 5:10:55 PM UTC-7, Alexey Kozlov wrote:

Hi Wayne,

this is very weird, source files are identical for Mac and Linux...

What compiler version are you using?
Are you trying to compile MPI version on Mac? (I guess I never tried it)
Does src/AncestralStates.cpp file look normal? (broken archive?)

Best,
Alexey

On 23.05.19 01:33, Wayne Pfeiffer wrote:
> Hi Alexey,
>
> After I downloaded
>
> 

> ra...@googlegroups.com <mailto:ra...@googlegroups.com>.

[Alexey Kozlov]

Hi Wayne,

> There must have been some problem with the files that I downloaded, since when I tried again, I was
> able to compile OK :) I still have been unable to get the executable to link to libpll, but I will
> work with someone here on that.

Great, let me know if I can help. A backup option would be to clone RAxML-NG with "--recursive" and
compile everything from source:

https://github.com/amkozlov/raxml-ng/wiki/Installation#building-from-source

> In answer to your first two questions, I have compiled with both gcc 7.2.0 and intel 2016.3.210 on
> our Comet supercomputer, which has Intel Haswell cores.

Thanks, I tested compilation with gcc 7.3.0 on our system and it worked.

Best,
Alexey

> > ra...@googlegroups.com <javascript:> <mailto:ra...@googlegroups.com <javascript:>>.

> > To view this discussion on the web visit
> >
> https://groups.google.com/d/msgid/raxml/f0c69637-0729-4e58-b6cf-371b0b8e7f94%40googlegroups.com
> <https://groups.google.com/d/msgid/raxml/f0c69637-0729-4e58-b6cf-371b0b8e7f94%40googlegroups.com>
> >

> <https://groups.google.com/d/msgid/raxml/f0c69637-0729-4e58-b6cf-371b0b8e7f94%40googlegroups.com?utm_medium=email&utm_source=footer
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>
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>
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