Add ignore_missing_alns option to TreeAnc to extend use cases

[corneliusroemer]

Resolves #177

Context
When doing ancestral state reconstruction with a tree that has many tips without alignment (>1/3), treetime throws an error.

This PR introduces a new constructor parameter ignore_missing_alns=False that defaults to False in a backward compatible manner. Setting it to true means that no error is raised even when more than 1/3 of tips don't have alignments attached.

This extends use cases.

Testing
Tested with my script that needs this feature and both True and False do exactly what they're supposed to do. No error vs error.

Usage

tt = TreeAnc(tree=tree, aln=alignment, ignore_missing_alns=True)

Other commits

I noticed that defaults weren't documented in numpy style in the docs, so I fixed it where I saw it. Also fixed a typo and indentation.