Thus, SPALSH is able to overcome some of the limitations of linear multiple-sequence aligners, and specifically it does not discard sites due to varying module grammar, or neutral mutations.
We consequently decided to conservatively discard sites whose evolutionary rate was above the arbitrary threshold of 2.2 (red line, Fig.2), in the hope of reducing risks of reconstruction artefacts.
Since true adaptive mutations are expected to be present in both lineages, we analyzed each lineage separately, discarding sites that are not shared by both human influenza lineages.
A matched control set of 40,000 random sites was generated in silico on the human genome by discarding sites with the nearest Tsp509I, HpyChIV4, or HinP1 recognition site at <20 bp (the minimum requirement for a blast search) or >500 bp (the maximum estimated length for efficient 454 bead loading).
Because our crossing scheme produced individuals isogenic for the third chromosome, we discarded sites called as heterozygous as they are likely misaligned reads located in highly repetitive regions.
Given the uncertainty about the samples and due to limited coverage, we discarded sites known to harbor such SNPs based on the 1000 Genomes Project data, to partially circumvent this problem (26, 67).
To compute CRERs significance, we kept sites with a maximal p-value of 10-4, and imposed a distance of at least six nucleotides between consecutive sites to discard overlapping sites that would bias the computed significance.
The sand, used by the foundry and discarded on site, is considered to be solid waste rather than hazardous material by the Connecticut Department of Environmental Protection.
The same students also made the structural frame of the house, crafting columns and beams from sheets of plywood discarded from site hoardings and concrete shuttering.
Removed plants are discarded off site.
We conservatively chose to discard PSHET sites that were clustered within 10-bp windows among the wAnaINF genomes.
