pal2nal.pl without sequences
Hello everyone,
I have been using pal2nal.pl to convert the protein alignment into the corresponding codon nucleotide alignment.
But, I have noticed that some of my outputs only contain the header (without sequences). I checked over the protein alignment and the fasta file, both have the correct format and data.
Bellow is an example of the pal2nal.pl output
259 0 Aj653
Aj8118
Aj8858
Aj9142
Aj9347
Aj9715
Aj16385
Aj19443
Cl22263707
Dr24435811
Ec23482696
Ef08139741
Hs01123478
I hope someone can help me to figure out and fix this error.
Thanks!!
Yocelyn
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Please test with just one sequence, and if the error persists, edit you question and include the amino-acid and nucleotide sequences. For post readability, it is better if the sequences are short.
Thank you,
I'll try your suggestion right now.
Best,
Yocelyn
Your first fasta-file header is 259 0 Aj653. Where is ">"?
And I would suggest to use underscore instead of space " "
in your fasta_headers.
This is an example how usual output looks like:
http://kodomo.cmm.msu.ru/~anahita/Pr1/pal2nal.with_codemlka_ks.v3.cgi.html