Hi! I am trying to build a phylogeny using a mixture of mitochondrial and nuclear protein-coding genes and rRNA genes. Is it possible to specify the specific type of gene in the partition file? I am using RAxML through the CIPRES portal to create the phylogeny. Many thanks in advance!
Why want you do that? If you specify your partitions with the best-fit substitution model than it is not necessary.
Csaba Csuzdi, how do you select the best-fit substitution model using your partition file?
nope, first you should use e.g. jmodeltest (or other) to find the best-fit model for each partition and this can be added to the partition file (in MrBayes it looks like something so
charset COI = 1-658; charset 16S = 659-1184; charset ITS = 1185-1807; partition favored= 3: COI, 16S, ITS; set partition=favored; Prset statefreqpr=dirichlet(1,1,1,1); Lset applyto=(1) nst=6 rates=invgamma; Lset applyto=(2) nst=6 rates=invgamma; Lset applyto=(3) nst=6 rates=gamma;
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