Hello!
I am trying to build a Phylogenetic tree based on 16S rRNA sequences. I have created a file with aligned sequences using ClustalW (uploaded file). The sequences was trimmed by Trimal.
My command: phyml -i aligned_sequences_name.clw -d nt -m HKY85 -c 4 -a e -o l -b 100
Report: The number of taxa cannot be negative.
What should I changed in my file to run the program?
I haven't used phyml in a while but I thought the format needed to be phylip format. I'm not sure if it accepts clustal. But i might be wrong...
The most convenient option would be to open the file with another program, such as SeaView, which is a very good program for performing alignments. Once the file is opened, the program can convert it to other formats, such as FASTA. You can then use the free MEGA program to perform phylogenetic analyses. SeaView can also perform phylogenies, but MEGA is more recommended, as it allows you to select a wide variety of parameters.
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