We should check that dnafrag_ids exist
The "id_type" parameter is consistent between SeqMember::bioseq() and AlignedMemberSet::get_SimpleAlign()
SeqMember::bioseq() parameters don't have to be repeated
New method to print the alignment to a file
New option in get_SimpleAlign() to remove the filtered columns
New documentation for SeqMember::bioseq()
Updated load_cigars_from_file()

It can now understand several kings of id_types and does extra checks that
were only performed in the protein-tree pipeline MSA module.
Can use AlignedMemberSet::load_cigars_from_file()
Do not need Bio::AlignIO
Default should be "blastp"
Parameters for e77
fixup print_sequences_to_file
perlcritic
No escape branch by default

We want the mafft_himem to fail if it can't make it.
bugfix: cannot store a tag on an undefined tree

Also, we now store the list of members that have been removed as a tag
Let's use the new GeneTree::alignment() method
We still use HMMer v2
sequence_id can be used multiple times. Don't delete it from aln_string_hash
load_cigars_from_file() only checks the sequences if asked

It must be an option because programs like MCoffee do funny things with funny characters
bugfix: store_alternative_tree() after treebest