I have been trying to convert my fasta file to an interleaved phylip file in R for a phylogeny project. Currently I have been using the package phylotools, starting with function read.fasta() which takes my fasta file to a dataframe and then dat2phyip() which takes the dataframe to a phylip file. However, it can only output a sequential phylip and for later scripts I need interleaved.

So either an answer to:

(1) how to convert fasta to interleaved phylip?

OR

(2) how to convert sequential phylip to interleaved phylip

would be very much appreciated!