Phastweb: A web interface for evolutionary conservation scoring of multiple sequence alignments using phastCons and phyloP

Ritika Ramani; Katie Krumholz; Yi Fei Huang; Adam Siepel

doi:10.1093/bioinformatics/bty966

Phastweb: A web interface for evolutionary conservation scoring of multiple sequence alignments using phastCons and phyloP

Ritika Ramani, Katie Krumholz, Yi Fei Huang, Adam Siepel

Research output: Contribution to journal › Article › peer-review

45 Scopus citations

Abstract

Summary: The Phylogenetic Analysis with Space/Time models (PHAST) package is a widely used software package for comparative genomics that has been freely available for download since 2002. Here, we introduce a web interface (phastWeb) that makes it possible to use two of the most popular programs in PHAST, phastCons and phyloP, without downloading and installing the PHAST software. This interface allows users to upload a sequence alignment and either upload a corresponding phylogeny or have one estimated from the alignment. After processing, users can visualize alignments and conservation scores as genome browser tracks and download estimated tree models and raw scores for further analysis. Altogether, this resource makes key features of the PHAST package conveniently available to a broad audience.

Original language	English (US)
Pages (from-to)	2320-2322
Number of pages	3
Journal	Bioinformatics
Volume	35
Issue number	13
DOIs	https://doi.org/10.1093/bioinformatics/bty966
State	Published - Jul 1 2019

All Science Journal Classification (ASJC) codes

Statistics and Probability
Biochemistry
Molecular Biology
Computer Science Applications
Computational Theory and Mathematics
Computational Mathematics

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10.1093/bioinformatics/bty966

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title = "Phastweb: A web interface for evolutionary conservation scoring of multiple sequence alignments using phastCons and phyloP",

abstract = "Summary: The Phylogenetic Analysis with Space/Time models (PHAST) package is a widely used software package for comparative genomics that has been freely available for download since 2002. Here, we introduce a web interface (phastWeb) that makes it possible to use two of the most popular programs in PHAST, phastCons and phyloP, without downloading and installing the PHAST software. This interface allows users to upload a sequence alignment and either upload a corresponding phylogeny or have one estimated from the alignment. After processing, users can visualize alignments and conservation scores as genome browser tracks and download estimated tree models and raw scores for further analysis. Altogether, this resource makes key features of the PHAST package conveniently available to a broad audience.",

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AU - Ramani, Ritika

AU - Krumholz, Katie

AU - Huang, Yi Fei

AU - Siepel, Adam

PY - 2019/7/1

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AB - Summary: The Phylogenetic Analysis with Space/Time models (PHAST) package is a widely used software package for comparative genomics that has been freely available for download since 2002. Here, we introduce a web interface (phastWeb) that makes it possible to use two of the most popular programs in PHAST, phastCons and phyloP, without downloading and installing the PHAST software. This interface allows users to upload a sequence alignment and either upload a corresponding phylogeny or have one estimated from the alignment. After processing, users can visualize alignments and conservation scores as genome browser tracks and download estimated tree models and raw scores for further analysis. Altogether, this resource makes key features of the PHAST package conveniently available to a broad audience.

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Phastweb: A web interface for evolutionary conservation scoring of multiple sequence alignments using phastCons and phyloP

Abstract

All Science Journal Classification (ASJC) codes

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