test version with alignment trimming
trimming version of phyluce/generic_align.py, likely to discard
resolving conflict between working and master
Updated working version of alignment trimming code

Following update to trim Velvet contigs of low coverage (lowercase)
bases, update alignment trimming code to filter slightly differently and
also add 2nd and 3rd pass filtering.

1) Changes to old code: now the code looks for alignment edges by moving across alignment
columns and requiring that (over a 20 bp sliding window) 65% of sites
have data for each taxon and 75% of those sites having data are
conserved across taxa.  The "edges" are found at either end in the first
windowed position where this is true.  Stuff outside the edges gets
trimmed.

2) Added 2nd pass filtering: after the first pass, above, the code
examines alignment data on a taxon-by-taxon basis (i.e., row-by-row  of
the alignment).  The code compares each row to the consensus for the
entire alignment and computes the running average (sliding window)
of differences between the taxon it's on and the consensus for all taxa.
The code then trims edges at the point where it finds running average
values < 0.5 prior to the first running average values of 0.99.  It does this on both ends, and converts
anything outside these edges to the insertion character "-".  This
should really be the missing data character "?", but it shouldn't really
matter much.  Changing to the missing data character to "?" should not
be a problem if we decide it's important.

3) Added 3rd pass filtering: because the conversion of edges in 2nd pass
filtering to "-" can basically reset the alignment boundaries (so all
taxa can sometimes start or end with a run of insertions like "----"),
re-run the first pass filtering again on the 2nd pass results to find
the edges of the alignment.
update seqcap_align_2 for changes in generic align
Update generic align to trim on 5 conserved bases at ends

The previous method was not behaving as well as I would like.  The
current method does the following during 2nd pass filtering:

After the first pass, the code examines alignment data on a
taxon-by-taxon basis (i.e., row-by-row  of the alignment).  The code
compares each row to the consensus for the entire alignment and computes
the running average (5 bp sliding window) of differences between the
taxon it's on and the consensus for all taxa.  The code then trims edges
at the point where it finds 5 adjacent running average values of >0.99.
It does this on both ends, and converts anything outside these edges to
the insertion character "-".  This should really be the missing data
character "?", but it shouldn't really matter much.  Changing to the
missing data character to "?" should not be a problem if we decide it's
important.
update dialign and muscle methods to remove reference to consensus
update mafft method to remove reference to consensus and change alignment to --maxiterate

mafft was originally set to use '--auto'.  now set to '--maxiterate
1000' which is equivalent to FFT-NS-i
(http://mafft.cbrc.jp/alignment/software/algorithms/algorithms.html#GLE).
This is a good tradeoff between speed and accuracy.  The remaining "more
accurate" methods were crazy slow.  This makes the alignments a little
gappier, but I think that it performs better than --auto, which is what
i was using before.  It's only slightly slower.
Cleanup code by annotating generic align methods
update test data