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LANL-Bioinformatics / PhaME

Given a reference, PhaME extracts SNPs from complete genomes, draft genomes and/or reads. Uses SNP multiple sequence alignment to construct a phylogenetic tree. Provides evolutionary analyses (genes under positive selection) using CDS SNPs.
GNU General Public License v3.0
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ERROR: number of input seqs differ (aa: 41; nuc: 0)!! #22

Open Rhia15 opened 1 year ago

Rhia15 commented 1 year ago

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 commented 1 year ago

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