finalizeAlignments: Finalize the alignments
In fmichonneau/rsowh: rsowh - an R interface for the SO-WH test

Description Usage Arguments Details Value Author(s)

This function concatenate all the loci for a given replicate to produce a single alignment, that will then be used by RAxML to estimate the likelihoods of the constrained and unconstrained topology.

1	finalizeAlignments(prefix, nreps, pathin, pathout)

`prefix`	The prefix shared by all the files representing replicates.
`nreps`	The number of replicates that have been generated.
`pathin`	path (i.e., directory) indicating where the files for each locus and each replicates are located.
`pathout`	path (i.e., directory) indicating where the each of the concatenated replicates will be stored;