I'm trying to figure out if there is a good way to split an alignment by positions. For example, let's say I have a supermatrix alignment of 5000 positions, and I want to split it by 1-501, 502-4500, 45001-5000 and then drop those new alignments into a new file. So three files with each taxon but only the positions specified in each file. Is there an easy way to do this? The starting file could either be a fasta or phylip file.
This would be different than taking a fasta file with thousands of sequences and splitting it up so only 500 different sequences are in any given file (that's been talked about elsewhere on this forum).