file naming convention

[Jed]

Alexandros,

I'm sure it's been brought up before, but have you considered changing the file naming convention in RAxML? Default file sorting mixes output files together. The assigned filename ends up being in the ragged right of standard "ls -l" sorting, rather than in the more readable, and more conventional, left-hand side of the filename. Also, it would be very convenient to have a standard filetype ending that could be assigned to open with certain software (e.g a ".tree" file handle).

Jed

[Alexandros Stamatakis]

Dear Jed,

You have a point there.

The problem is that any changes in output files names will affect many
tools/pipelines that are wrapped around RAxML, hence it's probably
better not to change anything,

Alexis

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--
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

[Jenna Morgan Lang]

Wouldn't it be relatively easy for Jed to modify and recompile his own RAxML code to create whatever file names he wants?

[Alexandros Stamatakis]

that's true, a simple:

"grep RAxML_ *.c"

will identify most lines in the code that will require modification,

alexis