Sub-group alignment files:

Command lines used to obtain alignments are:

mafft --maxiterate 100 --localpair in.fasta > out.fasta
trimal -in in.fasta -out out.fasta -htmlout out.html -gt 0.2


SG_I full alignment (fasta)
SG_I trimed alignment (fasta)

SG_II full alignment (fasta)
SG_II trimed alignment (fasta)

SG_III full alignment (fasta)
SG_III trimed alignment (fasta)

SG_IV full alignment (fasta)
SG_IV trimed alignment (fasta)

SG_V full alignment (fasta)
SG_V trimed alignment (fasta)

SG_VI full alignment (fasta)
SG_VI trimed alignment (fasta)

SG_VIIa full alignment (fasta)
SG_VIIa trimed alignment (fasta)

SG_VIIb full alignment (fasta)
SG_VIIb trimed alignment (fasta)

SG_VIII-1 full alignment (fasta)
SG_VIII-1 trimed alignment (fasta)

SG_VIII-2 full alignment (fasta)
SG_VIII-2 trimed alignment (fasta)

SG_IX full alignment (fasta)
SG_IX trimed alignment (fasta)

SG_Xa full alignment (fasta)
SG_Xa trimed alignment (fasta)

SG_Xb full alignment (fasta)
SG_Xb trimed alignment (fasta)

SG_XI full alignment (fasta)
SG_XI trimed alignment (fasta)

SG_XIIa full alignment (fasta)
SG_XIIa trimed alignment (fasta)

SG_XIIb full alignment (fasta)
SG_XIIb trimed alignment (fasta)

SG_XIIIa full alignment (fasta)
SG_XIIIa trimed alignment (fasta)

SG_XIIIb full alignment (fasta)
SG_XIIIb trimed alignment (fasta)

SG_XIV full alignment (fasta)
SG_XIV trimed alignment (fasta)

SG_XV full alignment (fasta)
SG_XV trimed alignment (fasta)

Positive selection corrected alignment files:

SG_II-3-4_corrected.aln (fasta)

SG_III-3-4_corrected.aln (fasta)

SG_III-8-9_corrected.aln (fasta)

SG_Xa-1-2_corrected.aln (fasta)

SG_Xb-5-6_corrected.aln (fasta)

SG_XI-14-15_corrected.aln (fasta)

SG_XI-17-18_corrected.aln (fasta)

SG_XI-19-20_corrected.aln (fasta)

SG_XI-8-9_corrected.aln (fasta)

SG_XIIa-2-3_corrected.aln (fasta)

SG_XIIIa-1-2_corrected.aln (fasta)

SG_XIIIb-1-2_corrected.aln (fasta)