The program AliStat was used to remove poorly aligned positions within the alignment with a mask value of 98 (55).
In a zebrafish/mouse/elephant shark sequences comparison, we defined by eye the unambiguously aligned regions within the alignment of the three sequences (see Figure 2, final 578 bp).
To prevent multiple fusions within the alignment, we restrict A s such that if a nucleotide in T is aligned to S or S′, none of the subsequent nucleotides in T can be aligned to G or G′ ensuring that T can be obtained by fusing at most two genes and there can be at most one 'transition' from G/ G′ to S/ S′.
However, as suggested by Wu et al. [ 55], these global column-specific approaches may mask well-aligned, phylogenetically informative sites within a particular clade, if other clades within the alignment have a poorer quality alignment for these sites.
The qualification instrument is thermally stable to operate during all mission phases around Mercury proving that the transmitter and receiver sections will remain within the alignment requirements during its mission.
No gaps were inserted within the alignment.
Gaps within the alignment were treated as missing data.
We used BLAT to align sequences to the human genome allowing for two mis-matches or gaps within the alignment [16].
Once the global alignment has been constructed, other methods are often used to identify the more conserved or reliable regions within the alignment.
First, the sequences were arranged into an alignment matrix, which defined the number of times each nucleotide was found at a specific position within the alignment.
This tree topology is probably an artefact of the asymmetric evolution of MyoD2 relative to other MyoD proteins, obscuring its true phylogenetic position by long branch attraction (LBA) or mutational saturation within the alignment.
