The increase in covariation is, in fact, due to the proportionally larger increase in positional entropy to joint entropy which is localized only to the misaligned positions.
Resulting alignments were purged from putatively misaligned positions as well as gap positions with Gblocks using default settings [ 36].
The resulting ribosomal protein alignments were inspected and adjusted manually for obviously misaligned positions using GeneDoc [ 45].
We discarded all cases in which we detected misaligned positions caused by the presence of large gaps or the use of isoforms containing alternative exons.
Although the aforementioned order of magnitude difference between error and distance would demand at most seven misaligned positions, we may have reached the resolution of the benchmark.
Here, we show that this approach is problematic because it increases the number of indels in the alignments due to the inclusion of nonhomologous regions, such as those derived from species-specific exons, increasing the number of misaligned positions.
Additionally, the resulting alignment was inspected by eye to correct obvious misaligned positions.
To demonstrate the increase in Zp, the 5-position misaligned block in Figure 3 was attached to the N-terminus of a triosephosephate isomerase alignment so Zp could be estimated.
However, when the ball eventually reaches the sensor hole, and awards you the amount of tickets indicated on the hole the ball dropped in, if the sensor that keeps track of the turntable's position becomes misaligned, the sensor may accidentally award you 100 Tickets, instead of the 3 that the ball landed.
Thirty-two positions where misaligned by NAST.
The number of aligned positions is the same in both cases but d N/d S is much higher in Longest, indicating that some positions are misaligned.
