Recently I have been working on using PAML to infer Ka/Ks values from different homologous sequences. The problem arose when i tried to run the program with 10 different sequences. After some troubleshooting, I found out that 3 of the 10 sequences (Bat, eleshrew and pig) are causing the program to kill or not run correctly.
The protein / nucleotide sequences were all downloaded from NCBI and then aligned using Pal2Nal and then MUSCLE.
Anyone know what can be causing the runtime error, and if so, a fix? The tests I am using are the M0 and the Branch tests. I am running with the following control file.
Thank you for your time and answers.
My unrooted tree file is:
Lastly this is the input protein homologous sequences.
Thank you to whoever can help me get over this. It is very much appreciated!
Feel free to ask any questions, I will answer to the best of my abilities.