on -m, -b and -p flags

[bio...@gmail.com]

Hi specialists,

I am new both to phylogenetics and RAxML, I have 3300 items of amino acids sequences and each item has 300-400AA length.

I want to use RAxML to build tree, but I am not sure what the appropriate flags are for -m, -b and -p flags. Should I use as large number for -b and -p flags as possible?

`which mpirun` -np 96 `which raxmlHPC-HYBRID-SSE3` -f d -m PROTCATBLOSUM62X -s aln.fasta -p 1333 -b 1335 -n aln_ro -N 96

Could anyone help me with that? Thank you!

Best wishes,

Jianhao

[Alexandros Stamatakis]

Dear Jianhao,

> I am new both to phylogenetics and RAxML, I have 3300 items of amino
> acids sequences and each item has 300-400AA length.
>
> I want to use RAxML to build tree, but I am not sure what the
> appropriate flags are for -m,

-m you can use Modeltest to determine an appropriate protein
substitution model, but you should also read a standard text book about
phylogenetics, e.g., the one by Ziheng Yang.

Typically the LG4M or LG4X models fit AA data best.

>-b and -p flags. Should I use as large
> number for -b and -p flags as possible?

-p is a random number seed so the size does not matter.

The same holds for -b.

>
> `which mpirun` -np 96 `which raxmlHPC-HYBRID-SSE3` -f d -m
> PROTCATBLOSUM62X -s aln.fasta -p 1333 -b 1335 -n aln_ro -N 96



>
> Could anyone help me with that? Thank you!
>
> Best wishes,
> Jianhao
>

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--
Alexandros (Alexis) Stamatakis

Research Group Leader, Heidelberg Institute for Theoretical Studies
Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology

www.exelixis-lab.org