I recently learned Pal2Nal is a good tool to align nucleotide sequences for subsequent downstream analyses involving positive selection. But I don't know how to use it from command-line. The webserver of the tool require to upload protein alignments and corresponding nucleotide sequences(unaligned). I have thousands of sequences and it is impossible for me to use the web based tool and my boss has suggested I use the commandline version to which I should write a python script to do the alignment and "include some lines in the script to feed the resulting codon alignment to "codeml" program to calculate Ka, Ks values".
Could anyone please help me how to proceed? I can use python but I don't know what types of arguments are acceptable by a commandline version of the tool. Any resource or help will be appreciated. Thanks