Sentence examples for settings to remove from inspiring English sources
The resulting protein alignments were reverse-translated to codon-based nucleotide alignments using PAL2NAL [ 47], which used the corresponding DNA sequences for positive selection analysis (see below), and another set of protein alignments were filtered by GBLOCKS [ 48] using default settings to remove regions that contained gaps or were highly divergent.
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The alignments were filtered by Gblocks [48] using default settings to remove regions that contain gaps or are highly divergent.
Vcfutils.pl varFilter was applied under default settings to remove low quality SNPs, with the addition of a minimum read depth of 10 [ 105].
Fastx_artifacts_filter was run with default settings to remove reads consisting of > 90% homopolymers, followed by fastq_quality_filter with the following options: −q 16 -p 90, meaning at least 90% of bases in a read needed quality scores of at least 16 for the read to be retained).
To avoid artificial alignment errors, we used Gblocks v.0.19b [ 80] with the following settings to remove ambiguous alignments: 26 minimum conserved positions, 42 minimum flanking positions, 8 maximum non-conserved positions, and a minimum length of a block of 5 while allowing gap positions in half.
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Due to the spatial sub-setting routine to remove data outside of Ethiopia, in addition to the calculation of monthly normal, the size of this entire data set was reduced from 23.6 GB to 210 MB.
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Gblocks (version 0.91) [48] with the default settings was used to remove alignment regions that contain gaps or are highly divergent.
