We find the three most informative ratios are for: 1) all possible TA contigs (all CRR), 2) the longest TA contig per ortholog (longest CRR), and 3) the sum of the ortholog length covered by all the TA contigs, which is then divided by the full length of the ortholog (sum CRR).
The resulting data sets comprised 27 specimens and 12 haplotypes with 777 characters (88 parsimony informative, ts/tv ratio = 1.941) for the M1M6 partition and 46 specimens, 13 haplotypes with 363 nucleotides (53 parsimony informative, ts/tv ratio = 1.65) for the I3M11 partition (Table S1).
It comprised 27 specimens and 12 haplotypes with 1140 characters (138 parsimony informative, ts/tv ratio = 1.685) and was used for the phylogenetic reconstruction of the COI gene (Fig. 2).
Over half (4083 of 7542) of all genes were excluded from further analysis because none of the 14 samples had more than one informative allelic ratio.
Full factorial designs (FFD) are used to simulate liquid foods since the FFD can suggest the most informative mixing ratios of ingredients.
We refer to the original publication for the other aspects of imputation, spot quality and filtering, but, like in Lapointe et al's study, they also filter to keep informative (expression ratios of benign versus cancer should at least be 1.5-fold or greater in at least half of one of the Gleason groups as one of the selection criteria).
With COII (positions 577 1591, 129 informative characters, ti/tv ratio 0.2000 6.0000), the MP analysis gave eight trees.
MP analysis of the ITS-1 sequences (positions 1592 2454, 169 informative characters, ti/tv ratio 0.6000 7.0000) gave 32 trees, one of which was retained after successive weighting.
Since the fetus has to be heterozygous for the SNP to be informative for allelic ratio analysis, the use of multiple markers is required to increase the population coverage.
The signal intensity is the most critical parameter that influences the informative value of ratio estimates [ 26].
The program is also designed to trim flanking sequences if they are not informative (if the ratio of maximum frequency to minimum frequency is <3).
