Alignments having only one condition

How should we deal with alignments containing species assigned to only one condition ?

We currently trim the tree to contain only species found in the alignment. Previous to commit bca26b31, Multinomial gave p = 1 when no or only one condition was found for a given site, resulting in the site being filtered out. This line broke this behavior, raising an exception when no or only one condition was found, without considering that this case could show up in normal usage.

We could easily revert this, although giving up early when detecting at the alignment level that less than 2 conditions were found could be a minor improvement, without relying on multinomial.

Example : ENSG00000197487_GALP_NT.fasta does not contain echolocating species