PHAST pipeline

PHAST specifications


Unique identifier OMICS_01557
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


  • PhastCons



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  • person_outline PHAST <>
  • person_outline Adam Siepel <>

Additional information

An R interface of PHAST is available on:

Publications for PHylogenetic Analysis with Space/Time models

PHAST IN pipelines

PMCID: 5596466
PMID: 28899353
DOI: 10.1186/s12864-017-4115-6

[…] as 2.5 kb around the most 5′ tss (2 kb upstream and 0.5 kb downstream from tss) of any refgene record. intergenic regions were defined as regions between neighboring refgene loci., the nine-way phastcons conserved elements file in rn4 format was downloaded from the ucsc genome browser. using bedtools [79], tsdmrs were overlapped with the conserved element track. genetic conservation […]

PMCID: 5615350
PMID: 28858207
DOI: 10.3390/genes8090216

[…] in each of the selected bac clones. by using multiple alignments, including all available cetartiodactyl genomes, we calculated the nucleotide conservation scores and conserved elements using phastcons [31]. then, we compared the characteristics of four bacs that had previously worked on distant species with all the 73 bacs by using the classification tree from the cart algorithm [32]. […]

PMCID: 5796051
PMID: 29286332
DOI: 10.3390/ijms19010101

[…] (release 27; used both pfam a and pfam b) [47]. any transcript with a pfam hit was excluded in the following steps, and pfam searches used default parameters of ‘-e 0.001’ and ‘--dome 0.001’., the phast (v1.3) software package contains several statistical programs that are used in phylogenetic analysis [48], and phastcons uses conservation scoring and an identification program of conserved […]

PMCID: 5890388
PMID: 29657298
DOI: 10.3390/ncrna4010001

[…] were estimated and compared 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 […]

PMCID: 4979189
PMID: 27506932
DOI: 10.1186/s12864-016-2975-9

[…] gene annotations from refseq [30] and ensembl [31] for the rat (rn5); these were downloaded from the table browser function in the ucsc genome browser [54]. we also used highly conserved regions (phastcons score = 1.0) [21] among 13 vertebrate species (multiz alignment of 13 vertebrates), which were also downloaded from the ucsc genome browser [55]. we merged all of these regions (i.e., […]

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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