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These alignments were checked by eye for alignment errors, poorly aligned regions were discarded.
Gblocks was used to remove poorly aligned regions of the alignments [ 61].
After using trimAl, we also visually inspected the trimmed alignments and removed poorly aligned regions.
Poorly aligned regions of the multiple protein alignment of EGFRs were removed with Gblocks49 using the least stringent parameters.
Resulting alignments were checked manually and poorly aligned positions excluded using MacClade v4.07 [45].
Whole genome alignments were also filtered for poorly aligned and gap regions using Gblocks 0.91b [ 64].
Poorly aligned sequences were manually removed from the alignment.
From these alignments we removed all codons from poorly aligned regions or those with insertion/deletions.
Poorly aligned and duplicated sequences were excluded from the alignment.
All alignments were manually inspected and short and poorly aligned sequences were removed.
We removed poorly aligned positions and divergent regions of a DNA alignment using Gblocks [ 23].
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