## This code is part of the megaptera package
## difference to mergeSubMSA:
## - does not write MSA into database
## - does not return subtree label but MSA
#' @export
mergeSubMSA2 <- function(megProj, subtree){
## PARAMETERS
## -----------
gene <- megProj@locus@sql
msa.tab <- paste(megProj@taxon@tip.rank,
gsub("^_", "", gene),
sep = "_")
merge.exe <- megProj@merge.exe
## read a pair of subMSAs from database:
subMSA <- lapply(subtree, dbReadDNA, x = megProj,
tab.name = msa.tab, regex = FALSE, subtree = TRUE)
## merge pair of subMSAs using OPAL:
opal.merge(subMSA, merge.exe)
}
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