Add FASTA as an input format

[rambaut]

Sequences in FASTA format (may require a separate input option)

[lskatz]

The nexus data format might be a drop in replacement (seqs + trees) but also I think nexus is probably overcomplicated.

[rambaut]

If it was highly constrained to a subset of the Nexus format it would be doable - I have written Nexus parsers a number of times. The main problem is it is overly flexible.

[lskatz]

Then it just makes sense with what you said -- fasta!

[rambaut]

Pushing this to a later version.