Phyphy

Includes a patch for FUBAR version 2.1, introduced in HyPhy version 2.3.9.

This release addresses a bug where nexus files were, under certain circumstances, read incorrectly when provided as a `data` argument to an Analysis method.

The argument `nexus=True` is now required when this type of input is provided, i.e.:

required here:
myfel = FEL(data = "data.nex", nexus=True)

but not required here:
myfel = FEL(alignment = "data.nex", tree = "data.tre")

This version marks the official, published release of phyphy.

Fixes a bug which produced incorrect output CSV when a non-comma delimiter is specified.

This release addresses a bug where executed LEISR instances could not be transferred to Extractor.

Includes new `Extractor()` methods for obtaining information from the JSON input field. Methods documented in README and API.