New likelihood-based phasing methods in Phaser

Phasing into PHASER

The guts of this package consist of the software contained in the diskette that accompanies the text. However, the text is necessary until one becomes familiar with the operations. A subtitle expands as follows: With a Supplementary Diskette Containing PHASER: An Animator/ Simulator for Dynamical Systems for IBM Personal Computers. This tells the potential reader and user basically what to expe...

phASER: Long range phasing and haplotypic expression from RNA sequencing

Map-likelihood phasing

The recently developed technique of maximum-likelihood density modification [Terwilliger (2000), Acta Cryst. D56, 965-972] allows a calculation of phase probabilities based on the likelihood of the electron-density map to be carried out separately from the calculation of any prior phase probabilities. Here, it is shown that phase-probability distributions calculated from the map-likelihood func...

Rare variant phasing and haplotypic expression from RNA sequencing with phASER

Haplotype phasing of genetic variants is important for clinical interpretation of the genome, population genetic analysis and functional genomic analysis of allelic activity. Here we present phASER, an accurate approach for phasing variants that are overlapped by sequencing reads, including those from RNA sequencing (RNA-seq), which often span multiple exons due to splicing. Using diverse RNA-s...

Phaser crystallographic software

Phaser is a program for phasing macromolecular crystal structures by both molecular replacement and experimental phasing methods. The novel phasing algorithms implemented in Phaser have been developed using maximum likelihood and multivariate statistics. For molecular replacement, the new algorithms have proved to be significantly better than traditional methods in discriminating correct soluti...