I have alignment in which some sequences are complete and start from first nucletide in the codon but some are shorter and start from 2 or 3 nucletide in the codon. Does codonphyml automatically treat this incomplete codons as a missing data or I have to make these sequences starting from full codon?
By the way, any chance for codonphyml to be intalled on some public computational resources such as CIPRES?
Best
Marcin
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Hi Marcin, sorry for the late reply. Moved to another place last semester, and did not have much time to look into codonphyml.
Not sure if I understood the first question correctly. I can say that codonphyml has no option to mark missing nucleotide sites in a sequence. The work around is to write a script to add gaps where nucleotides are missing.
We will go through some updates soon...will take a look on how to add codonphyml to CIPRES.
Best wishes for 2016!
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Hi,
I have alignment in which some sequences are complete and start from first nucletide in the codon but some are shorter and start from 2 or 3 nucletide in the codon. Does codonphyml automatically treat this incomplete codons as a missing data or I have to make these sequences starting from full codon?
By the way, any chance for codonphyml to be intalled on some public computational resources such as CIPRES?
Best
Marcin
Hi Marcin, sorry for the late reply. Moved to another place last semester, and did not have much time to look into codonphyml.
Not sure if I understood the first question correctly. I can say that codonphyml has no option to mark missing nucleotide sites in a sequence. The work around is to write a script to add gaps where nucleotides are missing.
We will go through some updates soon...will take a look on how to add codonphyml to CIPRES.
Best wishes for 2016!