1.7.7 Tree-related fixes

This addresses the following Issues:

CHANGES IN VERSION 1.7.7
-------------------------

USER-VISIBLE CHANGES

	- Tree fixes:

	- If a tree has NA branch-length values, they are automatically set to
0.
		This occurs within both phyloseq(), and read_tree().

	- UniFrac calculations require a rooted tree. While a rooted tree is
		not required to be part of a phyloseq object, it is a helpful
		default behavior to select a random root when UniFrac is called
		and the tree is unrooted, flashing a notice to the user.

	- Precise import from ape-package, rather than full-import.
		Smaller chance for collisions.
		Precisely-defined dependencies listed in NAMESPACE

	- As a result of the previous, phyloseq defines a placeholder "phylo"
class,
		extended from "list". This seems to match the class
		from a full import of ape, and is necessary since ape does not
		export the "phylo" class.
1.7.7 NEWS issues references

CHANGES IN VERSION 1.7.7
-------------------------

USER-VISIBLE CHANGES

	- Tree fixes:
		https://github.com/joey711/phyloseq/issues/235
		https://github.com/joey711/phyloseq/issues/255

	- If a tree has NA branch-length values, they are automatically set to
0.
		This occurs within both phyloseq(), and read_tree().

	- UniFrac calculations require a rooted tree. While a rooted tree is
		not required to be part of a phyloseq object, it is a helpful
		default behavior to select a random root when UniFrac is called
		and the tree is unrooted, flashing a notice to the user.

	- Precise import from ape-package, rather than full-import.
		Smaller chance for collisions.
		Precisely-defined dependencies listed in NAMESPACE

	- As a result of the previous, phyloseq defines a placeholder "phylo"
class,
		extended from "list". This seems to match the class
		from a full import of ape, and is necessary since ape does not
		export the "phylo" class.
Merge pull request #258 from joey711/tree-fixes

1.7.7 Tree fixes. Precise ape-import dependency, rather than full