PHAST statistics

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Citations per year

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PHAST specifications

Information


Unique identifier OMICS_01557
Name PHAST
Alternative names PHylogenetic Analysis with Space/Time models, phastWeb
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Alignment, gene annotations, the assumed tree topology.
Input format GFF,BED,FA,MAF,
Output data Statistic plots for comparative and evolutionary genomics.
Operating system Unix/Linux, Mac OS, Windows
Programming languages C, C++, Shell (Bash)
License BSD 3-clause “New” or “Revised” License
Computer skills Advanced
Version 1.4
Stability Stable
Maintained Yes

Subtools


  • dless
  • exoniphy
  • phastBias
  • PhastCons
  • phastOdds
  • phyloFit
  • phyloP
  • prequel

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Documentation


Maintainers


  • person_outline PHAST <>
  • person_outline Katherine S. Pollard <>
  • person_outline Adam Siepel <>

Additional information


An R interface of PHAST is available on: http://compgen.cshl.edu/rphast/

Publications for PHylogenetic Analysis with Space/Time models

PHAST in pipelines

 (72)
2018
PMCID: 5830370
PMID: 29217778
DOI: 10.3324/haematol.2017.180778

[…] calculations were performed using standard prediction tools. the evolutionary conservation across species and the physicochemical difference between amino acids were estimated by phylop, phastcons and the grantham score, respectively. mutant clonal size was inferred from allelic frequencies and the total number of next-generation sequencing reads normalized to the ploidy level. […]

2018
PMCID: 5870951
PMID: 29584760
DOI: 10.1371/journal.pone.0194518

[…] transcript similarity, we defined a transcript that had at least one or more exons that overlapped with the exons of another transcript in a transcriptome as recovered/assembled., the average hg19 phastcons [] 100-way conservation value was calculated across all exon bases to define average conservation scores (value between 0 and 1000). average rna-seq expression and ribo-seq expression […]

2018
PMCID: 5871330
PMID: 29580384
DOI: 10.7554/eLife.31347.034

[…] conserved rna structures were predicted using the rnaz web server () using step size 10 and a window size of 200. sequence repeats were identified by repeatmasker () and conservation was assessed by phastcons and phylop () via the ucsc genome browser (dm6)., this paper was supported by the following grants:, http://dx.doi.org/10.13039/501100001822austrian academy of sciences to jürgen knoblich., […]

2017
PMCID: 5321795
PMID: 28221375
DOI: 10.1038/ncomms14529

[…] in old flies (), and five exhibited llc-like behaviour (). among these five, only one (hereafter ‘crescendo') is conserved across several insects according to the 27 insect alignment and associated phastcons analysis from ucsc genome bioinformatics (). while crescendo partially overlapped both a te and a pirna cluster annotation in the sense strand, the other four fully overlapped transposable […]

2017
PMCID: 5443641
PMID: 28560331
DOI: 10.1126/sciadv.1602404

[…] we searched for conserved elements within these regions by aligning them to the medium ground finch (geospiza fortis) reference genome (geofor1) using blat (). we subsequently downloaded the phastcons bird conservation track () from the ucsc (university of california santa cruz) genome browser (). phastcons scores range from 0 to 1 and represent the probability of a nucleotide belonging […]


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PHAST in publications

 (745)
PMCID: 5946474
PMID: 29747577
DOI: 10.1186/s12864-018-4754-2

[…] ultimately, the transcripts predicted with coding potential by any of the four tools were filtered out, and those without coding potential would to be our candidate set of lncrnas., the software phast (v1.3) [] was usually used for phylogenetic analysis to evaluate the sequence conservation of transcripts. then, we used the program phylofit to calculate phylogenetic models of the conserved […]

PMCID: 5954278
PMID: 29764394
DOI: 10.1186/s12864-018-4458-7

[…] zebrafish lncrnas are likely implicated in some of key biological processes in nucleus., we also evaluated the full-transcript conservation levels of those conserved zebrafish lncrnas using 8-way phastcons scores (fig. ). it was found that the phastcons scores of conserved zebrafish lncrna are close to that of zebrafish coding-gene, both of which are significantly greater than the entirety […]

PMCID: 5940821
PMID: 29739970
DOI: 10.1038/s41598-018-24203-7

[…] in supplementary figure 3., fut4 mrna has two predicted mir-125b binding sites (~100 nt apart) in its 3′ utr, whilst mcl1 mrna also contains a predicted mir-125b target site in its 3′ utr (fig. ). phastcons scores for fut4 and mcl1 mir-125b binding sites indicate that their seed regions are highly conserved in vertebrates (fig. ). klf4 mrna contains a predicted mir-10a binding site, […]

PMCID: 5937035
PMID: 29730990
DOI: 10.1186/s12915-018-0518-3

[…] and negative error rates. to improve prediction quality, several quality scores were calculated and examined, including fp p value, match score of the sequence to the motif, conservation scores (phastcons and phylop in both glire and placental mammals), and footprint occupancy scores (fos) [], with a few modifications. first, the length of the flanking shoulders was optimized to yield […]

PMCID: 5930951
PMID: 29716548
DOI: 10.1186/s12864-018-4692-z

[…] the major snp allele (additional file ) was cloned upstream of a minimal promoter directing luciferase gene expression []. sequences surrounding each conserved region were selected based on the phastcons 17-way vertebrate alignment dataset (mean = 885 bp, range = 105 bp to 2497 bp) []. the selected sequences were then separately transfected into each cell line, and luciferase activity […]


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PHAST institution(s)
Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
PHAST funding source(s)
Supported by US National Institutes of Health grants R01-HG008161 and R35- GM127070.

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