---

type: position_score

table:
  filename: vertebrate.phyloP46way.bw
  # format: tabix

  header_mode: none

  # defined by score_type
  chrom:
    index: 0
  pos_begin:
    index: 1
  pos_end:
    index: 2
  chrom_mapping:
    del_prefix: chr

# score values
scores:
  - id: phyloP46_vertebrates
    type: float
    desc: "The score is a number that reflects the conservation at a position."
    large_values_desc: "more conserved"
    small_values_desc: "less conserved"
    index: 3
    histogram:
      type: number
      number_of_bins: 100
      view_range:
        min: -20.0
        max: 10.0
      y_log_scale: True

default_annotation:
  - source: phyloP46_vertebrates
    name: phyloP46_vertebrates

meta:
  summary: |
    Conservation score based on the multiple alignment of 46 species using vertebrate species


  description: |
    
    phyloP (phylogenetic P-values) scores measure the evolutionary rate at individual nucleotides or other genomic elements, providing a statistical framework to determine whether a particular site is evolving at a rate that is slower or faster than expected under a neutral model of evolution.
    
    This score is derived from a method called [PHAST (Phylogenetic Analysis with Space/Time models)](http://compgen.cshl.edu/phast/), which uses multiple sequence alignments and phylogenetic trees to identify conserved elements across different species.

    Positive scores indicate conservation, meaning the site is evolving more slowly than expected under a neutral model (purifying selection). Negative scores indicate acceleration, meaning the site is evolving faster than expected (positive selection or fast evolution).

    PhyloP uses a likelihood ratio test to compare the likelihood of the observed data under a model of neutral evolution versus a model of constrained or accelerated evolution. The result is a P-value that reflects the statistical significance of the deviation from the neutral rate.

    [Pollard et al., Detection of nonneutral substitution rates on mammalian phylogenies, Genome Research 2009](https://genome.cshlp.org/content/20/1/110)

    Downloaded on: 07/13/24

    [https://hgdownload.soe.ucsc.edu/goldenPath/hg19/phyloP46way/vertebrate.phyloP46way.bw](https://hgdownload.soe.ucsc.edu/goldenPath/hg19/phyloP46way/vertebrate.phyloP46way.bw)

