This is my first post in the community, so first off, thanks for the time you spend in replying to people's queries. It's a great help and I've already learnt quite a bit from just reading through.
I'm trying to calculate the rates of evolution in my set of sequences and I've been learning to use the CodeML program that is a part of the PAML package. I have made my sequence file in the Phylip Interleaved format and I've made my phylogenetic tree in the Nexus format. Initially, I simply wanted to run the M0 model and play around with the parameters to get used to the system.
But I have one problem, the program appears to read the sequences and produces a results file in the right folder but the results file is empty (zero bytes). I ran some of the test sequences available online and the program works properly but I cannot for some reason get it to work on my sequences.
I tried using the Nexus file format but it produces the following error,
"Error in sequence data file: X at 102 seq 1.
Make sure to separate the sequence from its name by 2 or more spaces."
I looked into the sequence file with a text editor and cannot see any errors as far as I can tell but that's where I think the error lies.
To summarise, when I use the Phylip interleaved format, PAML produces an empty results file. When using Nexus or sequential formats, it returns an error message.
Has anyone faced this issue before and if so, how did you manage to solve it ? Are there any reliable methods of producing these sequence files ? So far, I've used MacVector, Ugene and the online sequence format converter, Readseq. In each case, the errors are the same. I would much appreciate any help.
Thanks in advance,