ERROR: number of input seqs differ (aa: 41; nuc: 0)!!

[Rhia15]

Hi,

I am having some troubles using the pal2nal function for an aligned amino acid file and a nucleotide sequence file. I have aligned my raw amino files with clustalo and i have my corresponding nucleic acid files with the exact same headers in the same order. However, when using the command line pal2nal.pl rawamino_aln.faa rawnucl.fna -output paml -nogap > cluster_2.pal2nal I get the following error on both the web and in my terminal:

ERROR: number of input seqs differ (aa: 41; nuc: 0)!!

I cannot seem to find a problem with the order or the header names as they match, so I am very confused as to why this didn't work and would be so grateful for any help :) Thank you!

[mshakya]

Hi @Rhia15 , can you post few sequence headers from both files? Also are you running these outside of phame or within it?