phyloP pipeline

phyloP specifications

Information


Unique identifier OMICS_13233
Name phyloP
Alternative name phylogenetic P-values
Software type Package/Module
Interface Command line interface
Restrictions to use None
Output data Some raw reject substitutions values and P-values to be computed separately in post processing.
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Version 1.4
Stability Stable
Maintained Yes

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Documentation


Maintainer


  • person_outline Katherine S. Pollard <>

Publication for phylogenetic P-values

phyloP IN pipelines

 (9)
2017
PMCID: 5596466
PMID: 28899353
DOI: 10.1186/s12864-017-4115-6

[…] conservation was defined when ≥20% of a tsdmr overlapped with elements in the nine-way track; otherwise the tsdmr was defined as genetically not conserved., forty six-way human (hg19) vertebrate phylop scores and 30-way mouse (mm9) vertebrate phylop scores were downloaded from the ucsc genome browser. since there were no phylop score files for rat (rn4), we used human vertebrate phylop […]

2017
PMCID: 5615350
PMID: 28858207
DOI: 10.3390/genes8090216

[…] was created [29]. bac clones with appropriate insert sizes (50–300 kbp) and genetic content (unique genes, less repetitive elements) were selected. bac sequence conservation was estimated from phylop data [30] in the human genome (“conservation” track in grch37/hg19 assembly). genome coordinates were converted from cow to human using the batch coordinate conversion (liftover tool) in ucsc […]

2017
PMCID: 5796051
PMID: 29286332
DOI: 10.3390/ijms19010101

[…] program of conserved elements. we used phylofit to compute phylogenetic models for conserved and non-conserved regions among species, and then applied the model and hmm transition parameters to phylop to compute a set of conservation scores for lncrnas and coding genes., the cis role refers to the acting of lncrna on neighbouring target genes. we searched coding genes 100 kb upstream […]

2017
PMCID: 5890388
PMID: 29657298
DOI: 10.3390/ncrna4010001

[…] using cufflinks [52]. cage data for analysis of htapas and htert tsss in gm12878 cells were downloaded from the encode consortium (encode accession number encsr000cka). , phastcons, phylocsf and phylop scores, based on multi-way alignment of 20 mammalian genomes, were aggregated over the htapas locus (chr5:1295329-1296947, 1619 positions), htert exons (nm_198253 exons annotated in hg38, […]

2015
PMCID: 4776709
PMID: 26715627
DOI: 10.1093/molbev/msv344

[…] from 4-fold degenerate sites in coding regions. stringent filtering followed by identifying conserved elements with phastcons resulted in 177,346 tcrs., new code was developed in the phast program phylop (pollard et al. 2010; hubisz et al. 2011) to implement the internal branch test (‐‐branch option). previously, it was possible to test a single terminal branch or an entire subtree. the null […]

phyloP institution(s)
Gladstone Institutes, University of California, San Francisco, San Francisco, CA, USA; Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY, USA; Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
phyloP funding source(s)
This work was supported by the National Institute of General Medical Sciences (grant GM82901) and by early career awards from the Alfred P. Sloan Foundation, the David and Lucile Packard Foundation, and the National Science Foundation (grant DBI-0644111).

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