Support for Nexus format as input in PhyloNext

[vmikk]

Currently, PhyloNext accepts phylogenetic trees in Newick format (due to its simplicity and widespread use).
However, our pipeline internally converts these Newick trees into Nexus format at one of the intermediate steps.
Given that both Newick and Nexus formats are provided in the outputs, there is a clear benefit to supporting Nexus as an input format directly.

[vmikk]

Feature implemented, will be available in PhyloNext 1.5.0

PhyloNext/bin/12_Prepare_Biodiverse_input.R

Lines 181 to 190 in 9ce6a66

	} else if (file_extension(PHYTREE) %in% c("nex", "nexus", "nxs", "Nexus")) {
	## Load Nexus tree
	cat("..Based on the file extension, the Nexus format detected\n")
	TREE <- ape::read.nexus(PHYTREE, force.multi = FALSE)
	if("multiPhylo" %in% class(TREE)){
	cat("WARNING: The supplied file contains multiple phylogenetic trees, only the first one will be used!\n")
	TREE <- TREE[[1]]
	}