enable proper parsing of trinity headers
get probe names using new function based on regular expressions versus string splitting
remove seqtools dependency
PEP8 cleanup
remove older get_name function that we replaced with regex
remove pdb import
do not indent getting dupes statement
update docs to reflect removal of --regex and --repl commands for default processing
remove get_name() function from code (not used)
Fix error in incomplete matrix formation

Previously, building an incomplete matrix would return all loci
as being in the matrix.  This would later be removed during
alignment, but best to fix the problem here.  Now loci are returned
for all taxa in the input list that have any data for a locus.
PEP8 cleanup
update to allow trinity contigs, use SeqIO in place of seqtools, and improve locus counting
PEP8 compliance
ensure consensus has only ACGTN
Merge branch 'working' of github.com:faircloth-lab/phyluce into working
make assemblo-trinity more user friendly
improve error handling of match_contigs_to_probes
fix Node to node for get_fastas_from_match counts
remove dialign comments from mafft aligner
change behavior when alignments get fully trimmed and output X to stdout and list of loci at end