Phylobook:从分子系统进化论中显示、注释和提取序列的工具。

IF 2.2 4区 工程技术 Q3 BIOCHEMICAL RESEARCH METHODS
Jeffrey C Furlong, Peter D Darley, Wenjie Deng, James I Mullins, Roger E Bumgarner
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引用次数: 0

摘要

随着来自不同病原体的序列数据量的增加,分析、注释和提取特定类群进行研究的手段变得更加困难。为了应对这些挑战,"Phylobook "应运而生。从序列比对文件开始,Phylobook 生成并显示系统发生树,旁边的荧光笔图显示突变的位置,并允许用户识别世系和重组体,注释和导出选定的序列子集进行下游分析。利用不同聚类方法创建的注释,可以帮助进行难以自动化的准确系谱分配。Phylobook 提供基于网络的显示,结合自动聚类和手动编辑,允许专家评估和校正谱系分配,并提取用于下游分析。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Phylobook: a tool for display, clade annotation and extraction of sequences from molecular phylogenies.
As the volume of sequence data from variable pathogens increases, means of analyzing, annotating and extracting specific taxa for study becomes more difficult. To meet these challenges for datasets with hundreds to thousands of taxa, 'Phylobook' was developed. Starting with a sequence alignment file, Phylobook generates and displays phylogenetic trees adjacent to highlighter plots showing the position of mutations, and allows the user to identify lineages and recombinants, annotate and export selected subsets of sequences for downstream analysis. Accurate lineage assignment, which is difficult to automate, is aided using annotations created by different clustering methods. Phylobook provides web-based display combined with automated clustering and manual editing to allow for expert assessment and correction of lineage assignments and extraction for downstream analysis.
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来源期刊
BioTechniques
BioTechniques 工程技术-生化研究方法
CiteScore
4.40
自引率
0.00%
发文量
68
审稿时长
3.3 months
期刊介绍: BioTechniques is a peer-reviewed, open-access journal dedicated to publishing original laboratory methods, related technical and software tools, and methods-oriented review articles that are of broad interest to professional life scientists, as well as to scientists from other disciplines (e.g., chemistry, physics, computer science, plant and agricultural science and climate science) interested in life science applications for their technologies. Since 1983, BioTechniques has been a leading peer-reviewed journal for methods-related research. The journal considers: Reports describing innovative new methods, platforms and software, substantive modifications to existing methods, or innovative applications of existing methods, techniques & tools to new models or scientific questions Descriptions of technical tools that facilitate the design or performance of experiments or data analysis, such as software and simple laboratory devices Surveys of technical approaches related to broad fields of research Reviews discussing advancements in techniques and methods related to broad fields of research Letters to the Editor and Expert Opinions highlighting interesting observations or cautionary tales concerning experimental design, methodology or analysis.
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