PHAST and RPHAST: phylogenetic analysis with space/time models

By Melissa J. Hubisz, Katherine S. Pollard, Adam C. Siepel. Briefings Bioinform., 2011

500 citations recorded by the source corpus.

Subfields: Genetics, Molecular Biology, Paleontology

View Paper: https://www.semanticscholar.org/paper/3f0d293fe4fb470d338ceecd4bc58da7367a1b55

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Genetics

1. Martin Kircher
2. Daniela M. Witten
3. Gregory M. Cooper
4. Jay Shendure
5. Brian J. O'Roak
6. Edward L. Braun
7. Ludovic Antoine Alexandre Orlando
8. M. Springer

In Molecular Biology

1. Martin Kircher
2. Jay Shendure
3. Daniela M. Witten
4. Gregory M. Cooper
5. Brian J. O'Roak
6. Eske Willerslev
7. Edward L. Braun
8. Ludovic Antoine Alexandre Orlando

In Paleontology

1. Edward L. Braun
2. Ludovic Antoine Alexandre Orlando
3. Gregory M. Cooper
4. M. Springer
5. J. Fjeldså
6. M. W. Bruford
7. C. Rahbek
8. C. McCain

Citations in the corpus

• A general framework for estimating the relative pathogenicity of human genetic variants (2014, methodology): “…annotations (e.g. mapability scores and segmental duplication annotation as distributed by UCSC 51,52 ; PhastCons and phyloP conservation scores 53 for three multi-species alignments 9 excluding the human reference sequence in score calculation; GERP++ single-nucleotides scores, element scores…”
• Comparative genomics reveals insights into avian genome evolution and adaptation (2014, methodology): “1) (59) can be used to detect non-neutrally evolving genomic fragments in a given set of branches based on the multiple sequence alignments.”
• Exome sequencing as a tool for Mendelian disease gene discovery (2011, unknown): “Implementations of this strategy include phastCONS 39 , phyloP and Genetic Evolutionary Rate Profiling (GERP) 40 .”