Advance articles alert 10 July 2019

1. QuanTest2: Benchmarking(标杆/标准基点) Multiple Sequence Alignments using Secondary Structure Prediction 

Fabian Sievers Desmond G Higgins

Bioinformatics, btz552, https://doi.org/10.1093/bioinformatics/btz552

Published:11 July 2019

Abstract

Motivation

Secondary Structure Prediction Accuracy (SSPA) in the QuanTest benchmark can be used to measure accuracy of a Multiple Sequence Alignment (MSA). SSPA correlates（因素/相关） well with the Sum-of-Pairs (SP) score, if results are averaged over many alignments but not on an alignment by alignment basis. This is due to a sub-optimal selection of reference and non-reference sequences in QuanTest.

Results

We develop an improved strategy for selecting reference and non-reference sequences for a new benchmark（基准/基准测试程序）, QuanTest2. In QuanTest2 SSPA and SP correlate better on an alignment by alignment basis than in QuanTest. Guide-trees for QuanTest2 are more balanced with respect to reference sequences than in QuanTest. QuanTest2 scores correlate well with other well established benchmarks.

Availability

QuanTest2 is available as http://bioinf.ucd.ie/quantest2.tar, comprises of reference and non-reference sequence sets and a scoring script.

 

 

2. MCMCtreeR: functions to prepare MCMCtree analyses and visualise posterior ages on trees

Mark N Puttick

Bioinformatics, btz554, https://doi.org/10.1093/bioinformatics/btz554

Published:11 July 2019

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Abstract

Summary

The fossil record is incomplete, so molecular divergence（差异） time analysis is a crucial tool in estimating evolutionary timescales. The software MCMCtree contained in the PAML software provides Bayesian methods to estimate divergence times of genomic-sized sequences. Here, I present MCMCtreeR, a flexible R package to prepare time priors for MCMCtree analysis and plot time-scaled phylogenies. The package provides functions to refine parameters and visualise time-calibrated node prior distributions （时间校准的节点先验分布）so that these priors accurately reflect confidence in known, usually fossil, time information. After the parameters have been chosen, the package produces output files ready for MCMCtree analysis. Following analysis, the package has tools to compare prior and posterior calibrated node（校准后的节点） age distributions and produce plots of the time-scaled phylogenies（系统发生）. The plotting functions allow for the inclusion of age uncertainty on time-scaled phylogenies, including the display of full posterior distributions on nodes. Options also allow for the inclusion of the geological timescale（地质时间尺度）, and these plotting functions are applicable（适用的，合适的） with posterior age estimates from any Bayesian divergence-time estimation software.

Availability

MCMCtreeR is an R package available on CRAN (https://CRAN.R-project.org/package=MCMCtreeR). MCMCtreeR depends on the R packages ape, sn, and stats4.