Added option to nexusIO to not interleave the file.

This was problematic when using seqmagick to perform some conversions, to phylogenetic
software that did not support interleaving mode, specifically popart and network.

This change will not alter current usage of the write alignment function, but it does
enable the option to have interleaved nexus files output.

This ```#TODO``` is now moot, shouldn't it be removed?