jessica's edits
fixed typos from casing and option parser, added minsize to synteny orth, added options to recur on synteny in syntenyvis
Merge branch 'master' into yjw
Merge branch 'master' into yjw
Added null colormap to treelib, added options (e.g. do not label leaves, draw diagonal edges) to treesvg
fixed typo in svg, added options to treesvg, updated treelib (added Tree name, changed add/remove node to notify children, added null colormap)
Added debug info to assert statements in treelib.  Added stroke-width to svg.
Modified tree-split to use optparse and to allow for no rerooting or for multiple reroots of the original tree.
Added some speciation functions to phylo.  Added ancestors/descendants to treelib.  Added bgfreq to alignlib.
Fixed replace_tree.
Fixed mistake when returnCost=True in phylo.recon_root.  Added function to treelib to return the number of rooted or unrooted binary trees.
Merge branch 'master' into 'yjw'
Added iter_trees and read_trees to treelib
Refactored tree-split to use recon_root.  Added MATLAB-like min and max functions to util.
Added zscores to stats.  Added tree_hash_names to phylo.
Added option to (1) have reconroot return cost, (2) to have reroot keep root name, (3) to have tree.write output dists for all nodes if any node has dist.  Fixed some TreeSearch methods.
Added dupcost/losscost to phylo.py
Fixed raxml bootstrapping result and stats.cdf
Added namefunc to tree write and read functions
Merge branch 'master' into 'yjw'