Make it possible to include datasets with protein but not nucleotide sequences

Issue #98 resolved
Casey Dunn
repo owner created an issue

At present, agalma cannot include a dataset for which nucleotide data are not available, even though many use cases of homologize and downstream pipelines do not consider nucleotide data directly.

It should be possible to load a protein dataset for which nucleotide sequences are not available, and to then run homologize and downstream phylogeny pipelines in protein mode without nucleotide data.

If a pipeline is run in nucleotide mode on a dataset for which nucleotide data are note available, it should fail gracefully and alert the user of the problem.

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