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In practice, BFAST can align 1 billion Illumina 55 base-pair reads in 24 hour period on a cluster containing 156 computer computational cores, with suitable amounts of RAM, which makes these alignments practical from a computer hardware point of view.
The Ae. comosa and P. sanctum elements are easy to align (1 bp length difference; 89% identity), as are the C. delileana and H. persica elements, though these differ in length (29 bp length difference, 94.4% identity excluding gaps; Fig. 2).
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We aligned H3 and COI sequences without gaps.
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Since I tried Ludwig back in 2017, I have been constantly using it in both editing and translation. Ever since, I suggest it to my translators at ProSciEditing.

Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com