add NJst to phybase
convert execute to execute many to speed up insertions
adding probe tiling code
Merge branch 'working' of github.com:faircloth-lab/phyluce into working
fix number of cores check so that it does not automatical go multicore
Turn on --adjustdirection in mafft to orient sequences

Previously, sequence orientation occurred from lastz matches and
orientation was stored in the sqlite database.  However, with smaller
probe sequences, orientation values can sometimes become confused.  The
better option is to have mafft orient strands prior to alignment, which
was not an option earlier.  Add --adjust direction to mafft string.
alter trimming code to correctly place missing data characters at ends of alignments where there are gaps
allow removal of _R_ designator added by mafft during strand orientation as part of locus name
adjust addition of missing data designators for MultipleSeqAlign and _R_ strand indicator added by mafft
add code to get many fasta lengths and output as CSV
largely working version of automated trinity assembly
update get_trimmed_alignments_from_untrimmed.py for updated trimming code
Merge branch 'working' of github.com:faircloth-lab/phyluce into working
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