RAxML and Fasta

[Robert Lucking]

Hi,

can RAxML accept Fasta files? If not, perhaps an option for a future
version? Would avoid the extra step of Fasta-Phylip conversion. By the
way, congrats on this program! You guys deserve the Nobel prize for
phylogenetic programming!

Robert

[Andre J. Aberer]

Hi Robert,

> can RAxML accept Fasta files?

I fear no and I guess, it is much easier to perform file conversion
outside RAxML than within the code.

I attached an almost-one-liner, that I usually use for that. It should
work on most fasta-files, but as always, it is a good idea to
double-check the output...

> If not, perhaps an option for a future version? Would avoid the extra
> step of Fasta-Phylip conversion. By the way, congrats on this program!
> You guys deserve the Nobel prize for phylogenetic programming!
>
> Robert

--
Best regards,
Andre

[Alexis]

Thanks Andre,

We will probably not implement a fasta parser in RAxML any time soon,
because there are other more pressing issues
to be addressed first. Andre, do you mind if I put your script on our
lab web-site for download?

Thanks,

Alexis

>  convert.sh
> < 1 KBAnzeigenHerunterladen
>
>  application_pgp-signature_part
> < 1 KBAnzeigenHerunterladen

[Andre J. Aberer]

Hi Alexi,

> Andre, do you mind if I put your script on our lab web-site for
> download?

Of course, please do so.

--
Best regards,
Andre J. Aberer

M.Sc. (Bioinformatics)
Scientific Computing Group

Heidelberg Institute for Theoretical Studies (HITS gGmbH)
Schloss-Wolfsbrunnenweg 35
D-69118 Heidelberg

Tel.: +49 6221 533 264
Fax: +49 6221 533 298
Email: andre....@h-its.org
WWW: http://www.exelixis-lab.org
http://www.h-its.org/english/research/sco/index.php

Amtgericht Mannheim / HRB 337446
Managing Directors: Dr. h.c. Dr.-Ing. E.h. Klaus Tschira, Prof. Dr.-Ing. Andreas Reuter

[A-A_lowie li]

Dear Prof. Alexi:

       I also wrote some matlab code for converting fasta to phylip, or phylip to fasta.
       Please feel free to share it, maybe some users will find it useful :)

Lowie

--
Without dream, life is incomplete!

[JK]

Just wondering if there are any plans to eventually include FASTA support in RAx out of the box? I know it's a basic thing to do and that there are always more pressing matters, I'm still curious though.

Best,
-Jacek

[Alexandros Stamatakis]

Hi Jacek,

I'll put it on the TODO list, but don't expect this to happen quickly,
there's practically no time left any more to do programming :-(

Alexis

--
Alexandros (Alexis) Stamatakis

Research Group Leader, Heidelberg Institute for Theoretical Studies
Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology
Adjunct Professor, Dept. of Ecology and Evolutionary Biology, University
of Arizona at Tucson

www.exelixis-lab.org

[Alexandros Stamatakis]

Hi Jacek,

I have just pushed RAxML version 7.4.1 to github.

It should now be able to also parse FASTA files.

I would greatly appreciate if you could test it a bit for me.

Here is the commit message:

"added a rudimentary FASTA file parser. If the alignment file passed via
-s does not look like a phylip file, RAxML will try to parse a
FASTA-formatted file"

Alexis


On Thu, 2012-09-13 at 08:51 -0700, JK wrote:

[JK]

Thanks for the feature, Alexis, it's much appreciated! I have tested it and it works like a charm so far - I couldn't fool it by using interleaved FASTA with variable length, randomly inserted newlines, duplicated labels or very long names, so I'd say it is nice'n'good. I will start using it regularly from now on and I'll hit you back if any problem arises. Thanks again!

-J

[Ingo Michalak]

Dear Alexis,

I just tried to compile the new code (all SSE3/normal/PTHREADS versions) on a mac and it always failed with this message:

Undefined symbols:

  "_getline", referenced from:

      _getnums in axml.o

      _getinput in axml.o

ld: symbol(s) not found

collect2: ld returned 1 exit status

make: *** [raxmlHPC] Error 1

As I understood from the other thread this is related to this FASTA parser?

Best

Ingo

[Simon Berger]

Hi Ingo,

the cause for this also seems to be lack of the getline function on osx. As a quick check, you could could test the win32 branch from my github repository. It should also work on mac, you just have to change the '#ifdef __MINGW32__' in line 608 to an '#if 1' to activate the replacement getline function constantly.

Simon

[Ingo Michalak]

Hi Simon,

yep, that helped. Compilation succeeded. Thank you!

Ingo

[Alexandros Stamatakis]

Hi Ingo,

I've just pushed Simon's code to the standard RAxML version on my
github.

Would you be so kind as to test this one as well?

Thanks,

Alexis

[Ingo Michalak]

Hi Alexis,

thank you! I could compile a SSE3.PTHREADS version of your code and one analysis is already running.

Best

Ingo