adding some genetree helpers - may move
change r1, r2 to read1, read2
check for trimmed alignment
add more information to alignment dropping
add assemblo
fix up get_args
more PEP8 changes
generic method for adding gaps
add code to split concatenated nexus by partition into individual files
report back when alignment lengths are < 100 bp
add re-rooting and shortname options to renaming code
add replacement of spaces in case of KeyError
move datastore to nsf
change read names back to what's expected
allow us to work with automatically assembled contigs and fix CSV output header
ensure we remove * from genome-enabled taxon names
allow generation of UCE contigs in silico using old probe (5k) file
cleanup cruft
replace --multiprocessing option with --cores option
ensure we remove locus names from alignments and update to MutipleAlignment