Question: Question About Input Tree In Paml Codeml
1
gravatar for cacaucenturion
6.4 years ago by
cacaucenturion210 wrote:

Hi, does anyone know whether the input tree for PAML codeml analysis should be got based on codon alignment or amino acid alignment? Thanks!

phylogenetics paml • 3.0k views
ADD COMMENTlink modified 6.4 years ago by Rahul Sharma600 • written 6.4 years ago by cacaucenturion210
2
gravatar for Rahul Sharma
6.4 years ago by
Rahul Sharma600
Germany
Rahul Sharma600 wrote:

Hi

For positive selection prediction (Codeml module of PAML), one needs to provide the species tree. The Ids of the tree should be same as in the alignment file. Alignment file can be generated by codon based alignments (prank-codon is the recommended package).

ADD COMMENTlink written 6.4 years ago by Rahul Sharma600

Thanks! If some parts of the tree are not well resolved and the protein tree does not correspond well to the species tree, or if gene duplication happens, what kind of tree should I prepare? Should it be inferred based on codon alignment or protein sequence alignment? Thanks!

ADD REPLYlink written 6.4 years ago by cacaucenturion210
1
gravatar for Josh Herr
6.4 years ago by
Josh Herr5.6k
University of Nebraska
Josh Herr5.6k wrote:

I'm a little confused by your question. PAML is a maximum likelihood phylogenetics program which can handle both nucleotide and protein data. The input would be an aligned data matrix of nucleotide or protein data and the output would be a nexus file corresponding to the phylogenetic tree (or trees). There should be no input tree, but perhaps there is an analysis in PAML that I am not aware of. It's not on my list of choices for best phylogenetics programs.

ADD COMMENTlink modified 6.4 years ago • written 6.4 years ago by Josh Herr5.6k

Sorry, I meant that I wanted to use PAML to infer positive selection using codeml.

ADD REPLYlink written 6.4 years ago by cacaucenturion210
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