PHAST statistics

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Citations per year

Number of citations per year for the bioinformatics software tool PHAST
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Tool usage distribution map

This map represents all the scientific publications referring to PHAST per scientific context
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Associated diseases

This word cloud represents PHAST usage per disease context
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Popular tool citations

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Protocols

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

Download


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Versioning


No version available

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 citations

 (984)
library_books

Genome wide analysis of differentially expressed profiles of mRNAs, lncRNAs and circRNAs during Cryptosporidium baileyi infection

2018
BMC Genomics
PMCID: 5946474
PMID: 29747577
DOI: 10.1186/s12864-018-4754-2

[…] ential 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 and non-conserved regions among species. PhastCons was used to compute the conservation scores of coding genes and lncRNAs. […]

library_books

Comprehensive analysis of coding lncRNA gene co expression network uncovers conserved functional lncRNAs in zebrafish

2018
BMC Genomics
PMCID: 5954278
PMID: 29764394
DOI: 10.1186/s12864-018-4458-7

[…] comparison of zebrafish lncRNA and human lncRNA or mouse lncRNA with BLASTN using a relatively non-stringent E-value threshold 10− 5. Zebrafish lncRNAs’ conservation levels were evaluated using 8-way PhastCons score [].Using expression profiles of all SRA runs, the tissue specificity of zebrafish lncRNAs’ gene expression was calculated by TSI (Eq. ).6TSI=maxxi∑ixiWhere TSI is the tissue specificit […]

library_books

The polymorphism rs6918289 located in the downstream region of the TREM2 gene is associated with TNF α levels and IMT F

2018
Sci Rep
PMCID: 5940861
PMID: 29740051
DOI: 10.1038/s41598-018-25553-y

[…] genomic and phylogenetic context of rs6918289 were determined on the Human genome (GRCh38.p10) using Ensembl browser. The putative regulatory role of rs6918289 was established using rSNPBASE, and the PhyloP score was obtained using PhyloP software. […]

library_books

A genome wide assessment of conserved SNP alleles reveals a panel of regulatory SNPs relevant to the peripheral nerve

2018
BMC Genomics
PMCID: 5930951
PMID: 29716548
DOI: 10.1186/s12864-018-4692-z

[…] oring 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 was me […]

library_books

Widespread intronic polyadenylation diversifies immune cell transcriptomes

2018
Nat Commun
PMCID: 5928244
PMID: 29712909
DOI: 10.1038/s41467-018-04112-z

[…] re expressed from significantly longer transcription units than non-IpA genes (one-sided Wilcoxon rank-sum test, P < 10−20 for both comparisons, Fig. ). 3ʹIpA atlas events have higher conservation by PhastCons in the sequence surrounding the polyadenylation signal compared to 5ʹIpA atlas events (one-sided Wilcoxon signed-rank test, P < 10−66; Fig. ); however, 5ʹIpA events still show higher conserv […]

call_split

Prevalence and Spectrum of BRCA1/2 Germline Mutations in Women with Breast Cancer in China Based on Next Generation Sequencing

2018
PMCID: 5936051
PMID: 29681614
DOI: 10.12659/MSM.905812
call_split See protocol

[…] hen-2; http://genetics.bwh.harvard.edu/pph2) and Sorting Intolerant From Tolerant (SIFT; http://sift.jcvi.org/index.html). The evolutionary conservation of VUS was predicted by phylogenetic p-values (PhyloP) and Grantham.PolyPhen-2 was used to estimate the possible effect of an amino acid substitution on the structure and function of BRCA1 and BRCA2 proteins. In this program, mutations are classif […]


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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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