Misleading output in RAxML_info w/ options -f e -m GTRCAT

[tamuri]

In typical runs with GTRCAT model, the final ML optmisation switches to GTRGAMMA.

When using -f e (estimate model & branch lengths on topology given by -t), the output reads Final GAMMA likelihood but this is, in fact, the GTRCAT likelihood.

There is other output stating "Likelihood of final tree will be evaluated and optimized under GAMMA" etc.

Related to line: https://github.com/stamatak/standard-RAxML/blob/c3ed74d272347c332468f41a186a52ebd26d1533/axml.c#L8389

[stamatak]

thanks asif, we might eventually correct it, as most effort is going into raxml-ng now ...

alexis

On 31.01.2018 18:03, Asif Tamuri wrote:

In typical runs with GTRCAT model, the final ML optmisation switches to GTRGAMMA.

When using |-f e| (estimate model & branch lengths on topology given by |-t|), the output reads /Final GAMMA likelihood/ but this is, in fact, the GTRCAT likelihood.

Related to line: https://github.com/stamatak/standard-RAxML/blob/c3ed74d272347c332468f41a186a52ebd26d1533/axml.c#L8389

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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

[tamuri]

Cheers, I thought that'd be the case. Bug report is mostly for others who think their numbers look odd...

[stamatak]

thanks asif :-)

alexis

On 31.01.2018 21:37, Asif Tamuri wrote:

Cheers, I thought that'd be the case. Bug report is mostly for others who think their numbers look odd...

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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