Fixed some typos preventing proper calculation of distance-variance matrices and TreeCollection trees using TrClSeq methods
Points lib/remote to new point on git submodule
Merge branch 'master' of github.com:kgori/treeCl
1 - Plotter object handles embedding and distance_matrix plots.
2 - Small fix to verbosity level 1 TreeCollection and Phyml calls
    so that a newline is added after all instances have run.
3 - Moved remote head to latest commit
Fix to alf.py where tree was being expanded 100x on every call
Pairwise tree dists are normalisable and mismatchable; gtp calls are working
Added bootstrap resampling method to sequence record
Important fix for sequence concatenation: missing data char changed to "X" from "N" - N is asparagine in amino acid sequences
Cluster-rotate back on line. Need to work on setup.py
added analysis tools
Working on an optimiser
Testing optimiser
Testing optimiser (bugs)
added Optimiser framework
add files from master
merged upstream
removed random dependency
history attribute now makes sense
history attribute now makes sense
added var method