Multiple sequence alignments
We used Mafft v. 7.475 (Katoh & Standley, 2013) to build three multiple
sequence alignments (MSA) per each gene family. First, we generated a
MSA (MSAc) with only complete sequences identified in D.
silvatica using the L-INS-i algorithm with options –localpair
–maxiterate 1000. Then, we built a second MSA (MSAf) for all
sequences (the full data set, comprise the complete and partial copies
identified in D. silvatica ) using the Mafft –addfragments
option (–keeplength) to align fragment (partial) sequences to the
previous computed MSAc. Finally, we also used the L-INS-i algorithm to
generate a third MSA for each family, which included the complete
sequences from D. silvatica and the curated members of the same
family annotated in the genome of Drosophila melanogaster Meigen,
1830 (MSAp).