pal2nal.pl without sequences

Question

[YocelynGG]

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

[h.mon]

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.

[YocelynGG]

Thank you,

I'll try your suggestion right now.

Best,

Yocelyn

[natasha.sernova]

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