After data collection, each trial was individually inspected for correct marker identification, and then run through a low-pass Butterworth filter with a 6 Hz cutoff.
Due to the low number of polymorphic sites in the nuclear data sets, point mutations, deletions and/or insertions were individually inspected.
After identified objects following thresholding were individually inspected by the same investigator in a blinded manner to confirm the object as a neuron or not, the number of ChAT-positive neurons in the Ch1/2 was counted using AxioVision imaging software with the AutoMeasure module (Zeiss).
Sample duplicates were individually inspected for genotype consistency.
Contigs were individually inspected for low-quality sequence, splice variants and chimeras, before ESTs were reassembled.
After quality filtering, the sequence chromatograms were individually inspected and variants were manually reviewed by at least two researchers.
On day 10, around 20 midguts were individually inspected by phase contrast microscopy, and oocysts were counted.
Specifically, items were individually inspected for missing values, distribution characteristics (mean, SD, skewness and kurtosis) and item difficulty.
The sequences were individually inspected for chimeras, short reads, E. coli and mitochondrial sequences which were subsequently removed.
Results from these analyses were individually inspected on the Phytozome, where the loci and protein annotation were obtained.
As the resolution of our annotation is at single base level and each gene was individually inspected, gene borders and splice sites could be set quite accurately.
