• 文献检索
  • 文档翻译
  • 深度研究
  • 学术资讯
  • Suppr Zotero 插件Zotero 插件
  • 邀请有礼
  • 套餐&价格
  • 历史记录
应用&插件
Suppr Zotero 插件Zotero 插件浏览器插件Mac 客户端Windows 客户端微信小程序
定价
高级版会员购买积分包购买API积分包
服务
文献检索文档翻译深度研究API 文档MCP 服务
关于我们
关于 Suppr公司介绍联系我们用户协议隐私条款
关注我们

Suppr 超能文献

核心技术专利：CN118964589B侵权必究
粤ICP备2023148730 号-1Suppr @ 2026

文献检索

告别复杂PubMed语法，用中文像聊天一样搜索，搜遍4000万医学文献。AI智能推荐，让科研检索更轻松。

立即免费搜索

文件翻译

保留排版，准确专业，支持PDF/Word/PPT等文件格式，支持 12+语言互译。

免费翻译文档

深度研究

AI帮你快速写综述，25分钟生成高质量综述，智能提取关键信息，辅助科研写作。

立即免费体验

T-BAS版本2.1：用于DNA序列进化定位以及在经过整理的树和自定义树上查看比对及标本元数据的基于树的比对选择工具包。

T-BAS Version 2.1: Tree-Based Alignment Selector Toolkit for Evolutionary Placement of DNA Sequences and Viewing Alignments and Specimen Metadata on Curated and Custom Trees.

作者信息

Carbone Ignazio, White James B, Miadlikowska Jolanta, Arnold A Elizabeth, Miller Mark A, Magain Nicolas, U'Ren Jana M, Lutzoni François

机构信息

Center for Integrated Fungal Research, Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, North Carolina, USA

Center for Integrated Fungal Research, Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, North Carolina, USA.

出版信息

Microbiol Resour Announc. 2019 Jul 18;8(29):e00328-19. doi: 10.1128/MRA.00328-19.

DOI:10.1128/MRA.00328-19
PMID:31320426
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC6639605/
Abstract

The Tree-Based Alignment Selector (T-BAS) toolkit combines phylogenetic-based placement of DNA sequences with alignment and specimen metadata visualization tools in an integrative pipeline for analyzing microbial biodiversity. The release of T-BAS version 2.1 makes available reference phylogenies, supports multilocus sequence placements and permits uploading and downloading trees, alignments, and specimen metadata.

摘要

基于树的比对选择器（T-BAS）工具包将基于系统发育的DNA序列定位与比对和标本元数据可视化工具相结合，形成一个用于分析微生物多样性的综合流程。T-BAS 2.1版本的发布提供了参考系统发育树，支持多位点序列定位，并允许上传和下载树、比对结果及标本元数据。

相似文献

1
T-BAS Version 2.1: Tree-Based Alignment Selector Toolkit for Evolutionary Placement of DNA Sequences and Viewing Alignments and Specimen Metadata on Curated and Custom Trees.T-BAS版本2.1：用于DNA序列进化定位以及在经过整理的树和自定义树上查看比对及标本元数据的基于树的比对选择工具包。
Microbiol Resour Announc. 2019 Jul 18;8(29):e00328-19. doi: 10.1128/MRA.00328-19.
2
T-BAS: Tree-Based Alignment Selector toolkit for phylogenetic-based placement, alignment downloads and metadata visualization: an example with the Pezizomycotina tree of life.T-BAS：用于基于系统发育的定位、比对下载和元数据可视化的基于树的比对选择器工具包：以盘菌亚门生命树为例
Bioinformatics. 2017 Apr 15;33(8):1160-1168. doi: 10.1093/bioinformatics/btw808.
3
An open-access T-BAS phylogeny for emerging Phytophthora species.新兴疫霉属物种的开放获取 T-BAS 系统发育。
PLoS One. 2023 Apr 3;18(4):e0283540. doi: 10.1371/journal.pone.0283540. eCollection 2023.
4
SATe-II: very fast and accurate simultaneous estimation of multiple sequence alignments and phylogenetic trees.SATe-II：一种非常快速且准确的同时估计多个序列比对和系统发育树的方法。
Syst Biol. 2012 Jan;61(1):90-106. doi: 10.1093/sysbio/syr095. Epub 2011 Dec 1.
5
EGenBio: a data management system for evolutionary genomics and biodiversity.EGenBio：进化基因组学和生物多样性的数据管理系统。
BMC Bioinformatics. 2006 Sep 6;7 Suppl 2(Suppl 2):S7. doi: 10.1186/1471-2105-7-S2-S7.
6
Visualizing phylogenetic tree landscapes.可视化系统发育树景观。
BMC Bioinformatics. 2017 Feb 2;18(1):85. doi: 10.1186/s12859-017-1479-1.
7
On the quality of tree-based protein classification.论基于树的蛋白质分类的质量。
Bioinformatics. 2005 May 1;21(9):1876-90. doi: 10.1093/bioinformatics/bti244. Epub 2005 Jan 12.
8
SEPP: SATé-enabled phylogenetic placement.SEPP：基于SATé的系统发育定位
Pac Symp Biocomput. 2012:247-58. doi: 10.1142/9789814366496_0024.
9
The effect of the guide tree on multiple sequence alignments and subsequent phylogenetic analyses.引导树对多序列比对及后续系统发育分析的影响。
Pac Symp Biocomput. 2008:25-36. doi: 10.1142/9789812776136_0004.
10
VCFtoTree: a user-friendly tool to construct locus-specific alignments and phylogenies from thousands of anthropologically relevant genome sequences.VCFtoTree：一个用户友好的工具，用于从数千个人类学相关基因组序列构建位点特异性比对和系统发育树。
BMC Bioinformatics. 2017 Sep 26;18(1):426. doi: 10.1186/s12859-017-1844-0.

引用本文的文献

1
Environmental and host plant effects on taxonomic and phylogenetic diversity of root fungal endophytes.环境和宿主植物对根部真菌内生菌的分类学和系统发育多样性的影响。
FEMS Microbiol Lett. 2025 Jan 10;372. doi: 10.1093/femsle/fnaf030.
2
Use their names: there are no basal, lower, or early diverging fungi.使用它们的名称：不存在基部真菌、低等真菌或早期分化真菌。
Mycologia. 2025 Mar-Apr;117(2):246-254. doi: 10.1080/00275514.2025.2460003. Epub 2025 Feb 28.
3
A pangenome analysis reveals the center of origin and evolutionary history of Phytophthora infestans and 1c clade species.

本文引用的文献

1
Identification and characterization of as the causal agent of Septoria leaf spot disease of stevia in North Carolina.鉴定并描述了 是北卡罗来纳州甜菊叶斑病的病原菌。
Mycologia. 2019 May-Jun;111(3):456-465. doi: 10.1080/00275514.2019.1584503. Epub 2019 Apr 15.
2
Multi-locus DNA sequence analysis, antifungal agent susceptibility, and fungal keratitis outcome in horses from Southeastern United States.美国东南部马匹的多位点 DNA 序列分析、抗真菌药物敏感性和真菌性角膜炎结果。
PLoS One. 2019 Mar 28;14(3):e0214214. doi: 10.1371/journal.pone.0214214. eCollection 2019.
3
Birth of an order: Comprehensive molecular phylogenetic study excludes Herpomyces (Fungi, Laboulbeniomycetes) from Laboulbeniales.
一项泛基因组分析揭示了致病疫霉和1c进化枝物种的起源中心及进化史。
PLoS One. 2025 Jan 24;20(1):e0314509. doi: 10.1371/journal.pone.0314509. eCollection 2025.
4
Host specialization and spatial divergence of bacteria associated with Peltigera lichens promote landscape gamma diversity.与地卷衣属地衣相关的细菌的宿主专一性和空间分异促进了景观伽马多样性。
Environ Microbiome. 2024 Aug 5;19(1):57. doi: 10.1186/s40793-024-00598-x.
5
High species richness in the lichen genus (): 34 species in the dolichorhizoid and scabrosoid clades of section , including 24 new to science.地衣属（ ）的物种丰富度高：在 组的长根状和粗糙状分支中有34个物种，其中包括24个新科学物种。
Persoonia. 2023 Jun;51:1-88. doi: 10.3767/persoonia.2023.51.01. Epub 2023 Aug 8.
6
Systematic revision of species of and hyperparasitic on Meliolales (Ascomycota) in the tropics.热带地区小煤炱目（子囊菌门）上的 和 重寄生菌物种的系统修订。
MycoKeys. 2024 Apr 11;103:167-213. doi: 10.3897/mycokeys.103.115799. eCollection 2024.
7
Cryptic functional diversity within a grass mycobiome.草菌生物多样性的隐匿功能。
PLoS One. 2023 Jul 20;18(7):e0287990. doi: 10.1371/journal.pone.0287990. eCollection 2023.
8
Cassava begomovirus species diversity changes during plant vegetative cycles.木薯双生病毒物种多样性在植物营养生长周期中会发生变化。
Front Microbiol. 2023 May 25;14:1163566. doi: 10.3389/fmicb.2023.1163566. eCollection 2023.
9
First Whole Genome Sequence and Flow Cytometry Genome Size Data for the Lichen-Forming Fungus Ramalina farinacea (Ascomycota).地衣形成真菌粉石蕊（子囊菌门）的首个全基因组序列及流式细胞术基因组大小数据
Genome Biol Evol. 2023 May 7;15(5). doi: 10.1093/gbe/evad074.
10
An open-access T-BAS phylogeny for emerging Phytophthora species.新兴疫霉属物种的开放获取 T-BAS 系统发育。
PLoS One. 2023 Apr 3;18(4):e0283540. doi: 10.1371/journal.pone.0283540. eCollection 2023.
一个新目的的诞生：综合分子系统发育研究将 Herpomyces（真菌，子囊菌门，外囊菌目）排除在外囊菌目之外。
Mol Phylogenet Evol. 2019 Apr;133:286-301. doi: 10.1016/j.ympev.2019.01.007. Epub 2019 Jan 6.
4
A novel proof of concept for capturing the diversity of endophytic fungi preserved in herbarium specimens.一种新颖的概念验证，用于捕获保存在植物标本馆标本中的内生真菌的多样性。
Philos Trans R Soc Lond B Biol Sci. 2018 Nov 19;374(1763):20170395. doi: 10.1098/rstb.2017.0395.
5
Using collections data to infer biogeographic, environmental, and host structure in communities of endophytic fungi.利用群落数据推断内生真菌群落中的生物地理、环境和宿主结构。
Mycologia. 2018 Jan-Feb;110(1):47-62. doi: 10.1080/00275514.2018.1442078.
6
Population structure and migration of the Tobacco Blue Mold Pathogen, Peronospora tabacina, into North America and Europe.烟草霜霉病菌种群结构与迁移：进入北美洲和欧洲。
Mol Ecol. 2018 Feb;27(3):737-751. doi: 10.1111/mec.14453. Epub 2018 Jan 26.
7
Global population structure and adaptive evolution of aflatoxin-producing fungi.产黄曲霉毒素真菌的全球种群结构与适应性进化
Ecol Evol. 2017 Sep 30;7(21):9179-9191. doi: 10.1002/ece3.3464. eCollection 2017 Nov.
8
PhyD3: a phylogenetic tree viewer with extended phyloXML support for functional genomics data visualization.PhyD3：一个具有扩展 phyloXML 支持的系统发育树查看器，用于功能基因组学数据可视化。
Bioinformatics. 2017 Sep 15;33(18):2946-2947. doi: 10.1093/bioinformatics/btx324.
9
IcyTree: rapid browser-based visualization for phylogenetic trees and networks.IcyTree：基于浏览器的快速进化树和网络图可视化工具。
Bioinformatics. 2017 Aug 1;33(15):2392-2394. doi: 10.1093/bioinformatics/btx155.
10
T-BAS: Tree-Based Alignment Selector toolkit for phylogenetic-based placement, alignment downloads and metadata visualization: an example with the Pezizomycotina tree of life.T-BAS：用于基于系统发育的定位、比对下载和元数据可视化的基于树的比对选择器工具包：以盘菌亚门生命树为例
Bioinformatics. 2017 Apr 15;33(8):1160-1168. doi: 10.1093/bioinformatics/btw808.