Ramani, R., Krumholz, K., Huang, Y. F., Siepel, A. (November 2018) PhastWeb: a web interface for evolutionary conservation scoring of multiple sequence alignments using phastCons and phyloP. Bioinformatics, 35 (13). pp. 2320-2322. ISSN 1367-4803
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. Availability: PhastWeb is freely available on the web at http://compgen.cshl.edu/phastweb/. The website provides instructions as well as examples.
| Item Type: | Paper |
|---|---|
| Subjects: | bioinformatics > genomics and proteomics > genetics & nucleic acid processing > genomes > comparative genomics bioinformatics > genomics and proteomics > computers > computer software |
| CSHL Authors: | |
| Communities: | CSHL labs > Siepel lab CSHL Cancer Center Program > Cancer Genetics and Genomics Program |
| Depositing User: | Matthew Dunn |
| Date: | 27 November 2018 |
| Date Deposited: | 20 Dec 2018 16:25 |
| Last Modified: | 15 Nov 2023 18:32 |
| PMCID: | PMC6596881 |
| Related URLs: | |
| URI: | https://repository.cshl.edu/id/eprint/37496 |
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