Dear ReserachGaters,
the work with PAL2NAL is never simple for me (maybe its just me). Is there any other program I can use for preparing a prot/nuc alignment for analyses with PAML?
Thanks and cheers:)
Hi, Victoria Shabardina
You may try MAFFT and MACSE2 plugins in PhyloSuite(https://dongzhang0725.github.io/) platform.
For MAFFT, PhyloSuite added a "codon" alignment mode, which can do the same thing as PAL2NAL, i.e. first translate your NUC data to PROT, then align the PROT, finally back-translate the PROT to NUC. You may access https://dongzhang0725.github.io/dongzhang0725.github.io/documentation/#5-2-1-Brief-example to see a brief example.
MACSE2 is mainly designed for codon alignment, and it can handle the frameshift mutation, so it's poweful for codon alignment. You may also find a brief example here: https://dongzhang0725.github.io/dongzhang0725.github.io/documentation/#5-3-1-Brief-example.
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