Question: Detailed instructions for how to use PAML
gravatar for dixex
3.1 years ago by
dixex0 wrote:

I would like to calculate the dn/ds ratio for a series of genes for 5 different species. I am trying to use PAML, but I'm having a difficult time figuring out how to use it. I've look at Yang's manual ( and other various tutorials, but the material is still over my head. I can't figure out how to get the multiple alignment sequence in the correct format and I don't understand what the treefile is all about, among other things. Does anyone have a detailed guide to using PAML for beginners?

dn/ds ratio paml file format • 6.2k views
ADD COMMENTlink modified 3.1 years ago by h.mon31k • written 3.1 years ago by dixex0
gravatar for h.mon
3.1 years ago by
h.mon31k wrote:

PAML is somewhat notorious for having a steep learning curve. You may try POTION or LMAP, which are supposedly easier wrappers around PAML. But my recommendation is to use ETE Toolkit 3, it makes it easy to automate PAML runs for several genes and it has some nice format manipulation and tree printing capabilities. See a short tutorial here.

ADD COMMENTlink written 3.1 years ago by h.mon31k

Thank-you! I will definitely look into these options, especially ETE Toolkit 3.

ADD REPLYlink written 3.1 years ago by dixex0
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