Hello, I'm trying to run a Maximum Likelihood analysis with RAxML, but after providing the concatenated data file (.phy) and the partition file inferred by IQ-Tree in .txt format, I'm encountering an error. RAxML returns: "not recognized as an internal or external command, operable program, or batch file."
Here is my partition file:
DNA, 12S_16S_COI_codon1_RAG1_codon3 = 1-972, 973-3544, 3546-4203\3, 4206-4659\3
DNA, COI_codon2_RAG1_codon1_RAG1_codon2 = 3547-4203\3, 4204-4659\3, 4205-4659\3
DNA, COI_codon3 = 3545-4203\3
And this is the command I run in RAxML:
raxmlHPC -s Pseudopaludicola_Concat_RaxML.phy -p 1234 -m GTRGAMMA -q
Particoes_Pseudopaludicola_raxml.txt -n Pseudopaludicola_best -# 1000
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