Things to fix before publication

[szitenberg]

pj.tree breakes with PbConf when placing the tree in p.trees *()
line 2644 for i in range(1,str(nchains)+1):: Change str to int
css in html report
NexML contains alignments
rf matrix (numbers no hitmap)~~~~Going with hitmaps after all
new stat plots in the report (or make sure axes are not cropped)
add git and pickle keyword to the function that reads nexus with charset
make sure the ipynb is in the report.
include exonerate and bayestraits in the image