Genomic scaffolds from 14 Drosophila species are aligned
against the D. melanogaster genome assembly (dm6) with LAST
using default parameters. The alignments are then processed using the
UCSC whole genome alignment protocol (i.e. chaining, netting, and maffing).
PhastCons (which has been used in previous Conservation tracks) is a hidden Markov model-based
method that estimates the probability that each nucleotide belongs to a conserved element, based
on the multiple alignment. It considers not just each individual alignment column, but also
its flanking columns. By contrast, phyloP separately measures conservation at individual
columns, ignoring the effects of their neighbors. As a consequence, the phyloP plots have a less
smooth appearance than the phastCons plots, with more "texture" at individual sites.
The two methods have different strengths and weaknesses. PhastCons is sensitive to "runs" of
conserved sites, and is therefore effective for picking out conserved elements. PhyloP, on the
other hand, is more appropriate for evaluating signatures of selection at particular nucleotides
or classes of nucleotides (e.g., third codon positions, or first positions of miRNA target sites).
Another important difference is that phyloP can measure acceleration (faster evolution than
expected under neutral drift) as well as conservation (slower than expected evolution). In the
phyloP plots, sites predicted to be conserved are assigned positive scores (and shown in blue),
while sites predicted to be fast-evolving are assigned negative scores (and shown in red).
The absolute values of the scores represent -log p-values under a null hypothesis of neutral
evolution. The phastCons scores, by contrast, represent probabilities of negative selection and
range between 0 and 1.
Both phastCons and phyloP treat alignment gaps and unaligned nucleotides as missing data.
Missing sequence in the assemblies is highlighted in the track display by regions of yellow when
zoomed out and Ns displayed at base level (see Gap Annotation, below).
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