Problem reading alignment file

[NEELAM KUSHWAHA]

Hi, i am trying to run Raxml and give following error-.

/raxmlHPC -m PROTGAMMAWAG -p 12345 -s /home/bvs/neelam/RNDalnphylip.phy -# 20 -n T

ERROR: Bad base (_) at site 2 of sequence 1
Printing error context:

3
CP028959.1_4930 P_aeruginosa_IMP66resi

Problem reading alignment file

[Alexandros Stamatakis]

the problem seems to be the space between:

CP028959.1_4930 and P_aeruginosa_IMP66resi

try inserting an underscore there.

Also what is this 3 before

CP028959.1_4930 P_aeruginosa_IMP66resi

doing there?

RAxML can read FAST or extended phylip files.

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
Affiliated Scientist, Evolutionary Genetics and Paleogenomics (EGP) lab,
Institute of Molecular Biology and Biotechnology, Foundation for
Research and Technology Hellas

www.exelixis-lab.org