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HHProfileParser hhmake compatibility
HHMs created with HHsuite 2.0's hhmake can have a number of features that will cause an exception while loading with HHProfileParser.
The issues I noticed are: the master sequence of the profile, if the user has not set explicitly the -cons flag, may contain gaps. If the user has set the -cons flag, the process fails when loading additional sequences in the .hhm that have a different length
compared to the consensus sequence (because the consensus sequence only contains match states, whereas the alignment may also include insert columns).
It seems that these issues are due to the different HMM standards of HHsuite 2.0.