I need to generate a phylip outfile with the inferred ancestral DNA sequences at each node of a tree. Phylip provides this option, and the default setting returns a reference sequence (reconstructed at the ancestral node) and subsequent sequences denoted by "." if there is no change and by a nucleotide if there is a change, e.g.
1 ACTCATG
1,2 .......
2,3 ..A....
2,4 .......
etc.
Phylip also provides an option to list the entire node sequence rather than just the "." placeholders. It turns out that this is very helpful for counting the actual number of mutations in a tree when there are sequential mutations in nodes, because then there are two changes with respect to the reference sequence (in those cases, just knowing the ancestral reference sequence is insufficient, so you have to traverse the entire tree and reconstruct the sequences). Generating output sequences rather than the "." placeholders in phylip is straightforward - when you select the '5' option to return ancestral sequences, you're taken to a menu that lets you de-select the "." option and return a sequence.
However, I cannot figure out how to do this when running dnapars in the emboss wrapper. If I want to return an outfile with ancestral sequences, I run:
ednapars -sequence <infile.phy> -outfile <outfilename> -seqatnodes Yes
This returns the default "." notation for ancestral sequences. How can I specify an input argument to return the ancestral nucleotide sequence rather than the default placeholder dots?
