NewickTreeModifier: 用于修剪和修改 Newick 树的简单网页。

IF 3 2区生物学 Q2 EVOLUTIONARY BIOLOGY Journal of Heredity Pub Date : 2024-03-13 DOI:10.1093/jhered/esae005

Lynn Ogoniak, Raphael Steffen, Norbert Grundmann, Ben Stöver, Kai Müller, Jürgen Schmitz

{"title":"NewickTreeModifier: 用于修剪和修改 Newick 树的简单网页。","authors":"Lynn Ogoniak, Raphael Steffen, Norbert Grundmann, Ben Stöver, Kai Müller, Jürgen Schmitz","doi":"10.1093/jhered/esae005","DOIUrl":null,"url":null,"abstract":"Large-scale selection analyses of protein-coding sequences and phylogenetic tree reconstructions require suitable trees in Newick format. We developed the NewickTreeModifier (NTM), a simple web-based tool to trim and modify Newick trees for such analyses. The users can choose provided master trees or upload a tree to prune it to selected species available in FASTA, NEXUS, or PHYLIP sequence format with an internal converter, a simple species list, or directly determined from a checklist interface of the master trees. Plant, insect, and vertebrate master trees comprise the maximum number of species in an up-to-date phylogenetic order directly transferable to the pruned Newick outfile. NTM is available at https://retrogenomics.uni-muenster.de/tools/ntm.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":null,"pages":null},"PeriodicalIF":3.0000,"publicationDate":"2024-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"NewickTreeModifier: A simple web tool to prune and modify Newick trees.\",\"authors\":\"Lynn Ogoniak, Raphael Steffen, Norbert Grundmann, Ben Stöver, Kai Müller, Jürgen Schmitz\",\"doi\":\"10.1093/jhered/esae005\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"Large-scale selection analyses of protein-coding sequences and phylogenetic tree reconstructions require suitable trees in Newick format. We developed the NewickTreeModifier (NTM), a simple web-based tool to trim and modify Newick trees for such analyses. The users can choose provided master trees or upload a tree to prune it to selected species available in FASTA, NEXUS, or PHYLIP sequence format with an internal converter, a simple species list, or directly determined from a checklist interface of the master trees. Plant, insect, and vertebrate master trees comprise the maximum number of species in an up-to-date phylogenetic order directly transferable to the pruned Newick outfile. NTM is available at https://retrogenomics.uni-muenster.de/tools/ntm.\",\"PeriodicalId\":54811,\"journal\":{\"name\":\"Journal of Heredity\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":3.0000,\"publicationDate\":\"2024-03-13\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Journal of Heredity\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://doi.org/10.1093/jhered/esae005\",\"RegionNum\":2,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q2\",\"JCRName\":\"EVOLUTIONARY BIOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Journal of Heredity","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1093/jhered/esae005","RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"EVOLUTIONARY BIOLOGY","Score":null,"Total":0}

引用次数: 0

摘要

蛋白质编码序列的大规模选择分析和系统发生树的重建需要合适的 Newick 格式树。我们开发了 NewickTreeModifier，这是一种基于网络的简单工具，用于修剪和修改 Newick 树以进行此类分析。用户可以选择提供的主树，也可以上传一棵树，通过内部转换器、简单的物种列表或从主树的核对表界面直接确定，将其修剪为以 FASTA、NEXUS 或 PHYLIP 序列格式提供的选定物种。植物、昆虫和脊椎动物的主树包括可直接转移到经过修剪的 Newick outfile 的最新系统发生顺序中的最大物种数量。NTM 可在 https ：//retrogenomics.uni-muenster.de/tools/ntm.

本文章由计算机程序翻译，如有差异，请以英文原文为准。

查看原文

微信好友朋友圈 QQ好友复制链接

本刊更多论文

NewickTreeModifier: A simple web tool to prune and modify Newick trees.

Large-scale selection analyses of protein-coding sequences and phylogenetic tree reconstructions require suitable trees in Newick format. We developed the NewickTreeModifier (NTM), a simple web-based tool to trim and modify Newick trees for such analyses. The users can choose provided master trees or upload a tree to prune it to selected species available in FASTA, NEXUS, or PHYLIP sequence format with an internal converter, a simple species list, or directly determined from a checklist interface of the master trees. Plant, insect, and vertebrate master trees comprise the maximum number of species in an up-to-date phylogenetic order directly transferable to the pruned Newick outfile. NTM is available at https://retrogenomics.uni-muenster.de/tools/ntm.

求助全文

通过发布文献求助，成功后即可免费获取论文全文。去求助

来源期刊

Journal of Heredity 生物-遗传学

CiteScore

5.20

自引率

6.50%

发文量

审稿时长

6-12 weeks

期刊介绍： Over the last 100 years, the Journal of Heredity has established and maintained a tradition of scholarly excellence in the publication of genetics research. Virtually every major figure in the field has contributed to the journal. Established in 1903, Journal of Heredity covers organismal genetics across a wide range of disciplines and taxa. Articles include such rapidly advancing fields as conservation genetics of endangered species, population structure and phylogeography, molecular evolution and speciation, molecular genetics of disease resistance in plants and animals, genetic biodiversity and relevant computer programs.