BAD2matrix：系统基因组矩阵连接、索引编码等

IF 2.7 3区生物学 Q2 PLANT SCIENCES

Applications in Plant Sciences Pub Date : 2024-09-24 DOI:10.1002/aps3.11604

Nelson R. Salinas, Gil Eshel, Gloria M. Coruzzi, Rob DeSalle, Michael Tessler, Damon P. Little

{"title":"BAD2matrix：系统基因组矩阵连接、索引编码等","authors":"Nelson R. Salinas, Gil Eshel, Gloria M. Coruzzi, Rob DeSalle, Michael Tessler, Damon P. Little","doi":"10.1002/aps3.11604","DOIUrl":null,"url":null,"abstract":"<div>\n \n \n <section>\n \n <h3> Premise</h3>\n \n <p>Common steps in phylogenomic matrix production include biological sequence concatenation, morphological data concatenation, insertion/deletion (indel) coding, gene content (presence/absence) coding, removing uninformative characters for parsimony analysis, recording with reduced amino acid alphabets, and occupancy filtering. Existing software does not accomplish these tasks on a phylogenomic scale using a single program.</p>\n </section>\n \n <section>\n \n <h3> Methods and Results</h3>\n \n <p>BAD2matrix is a Python script that performs the above-mentioned steps in phylogenomic matrix construction for DNA or amino acid sequences as well as morphological data. The script works in UNIX-like environments (e.g., LINUX, MacOS, Windows Subsystem for LINUX).</p>\n </section>\n \n <section>\n \n <h3> Conclusions</h3>\n \n <p>BAD2matrix helps simplify phylogenomic pipelines and can be downloaded from https://github.com/dpl10/BAD2matrix/tree/master under a GNU General Public License v2.</p>\n </section>\n </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"12 6","pages":""},"PeriodicalIF":2.7000,"publicationDate":"2024-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11604","citationCount":"0","resultStr":"{\"title\":\"BAD2matrix: Phylogenomic matrix concatenation, indel coding, and more\",\"authors\":\"Nelson R. Salinas, Gil Eshel, Gloria M. Coruzzi, Rob DeSalle, Michael Tessler, Damon P. Little\",\"doi\":\"10.1002/aps3.11604\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div>\\n \\n \\n <section>\\n \\n <h3> Premise</h3>\\n \\n <p>Common steps in phylogenomic matrix production include biological sequence concatenation, morphological data concatenation, insertion/deletion (indel) coding, gene content (presence/absence) coding, removing uninformative characters for parsimony analysis, recording with reduced amino acid alphabets, and occupancy filtering. Existing software does not accomplish these tasks on a phylogenomic scale using a single program.</p>\\n </section>\\n \\n <section>\\n \\n <h3> Methods and Results</h3>\\n \\n <p>BAD2matrix is a Python script that performs the above-mentioned steps in phylogenomic matrix construction for DNA or amino acid sequences as well as morphological data. The script works in UNIX-like environments (e.g., LINUX, MacOS, Windows Subsystem for LINUX).</p>\\n </section>\\n \\n <section>\\n \\n <h3> Conclusions</h3>\\n \\n <p>BAD2matrix helps simplify phylogenomic pipelines and can be downloaded from https://github.com/dpl10/BAD2matrix/tree/master under a GNU General Public License v2.</p>\\n </section>\\n </div>\",\"PeriodicalId\":8022,\"journal\":{\"name\":\"Applications in Plant Sciences\",\"volume\":\"12 6\",\"pages\":\"\"},\"PeriodicalIF\":2.7000,\"publicationDate\":\"2024-09-24\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11604\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Applications in Plant Sciences\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://onlinelibrary.wiley.com/doi/10.1002/aps3.11604\",\"RegionNum\":3,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q2\",\"JCRName\":\"PLANT SCIENCES\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Applications in Plant Sciences","FirstCategoryId":"99","ListUrlMain":"https://onlinelibrary.wiley.com/doi/10.1002/aps3.11604","RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"PLANT SCIENCES","Score":null,"Total":0}

引用次数: 0

摘要

系统基因组矩阵生成的常见步骤包括生物序列拼接、形态学数据拼接、插入/删除（indel）编码、基因内容（存在/不存在）编码、去除无信息字符进行简约分析、用还原氨基酸字母记录和占用过滤。现有的软件不能使用单个程序在系统基因组规模上完成这些任务。方法和结果BAD2matrix是一个Python脚本，可以执行上述步骤，构建DNA或氨基酸序列以及形态数据的系统基因组矩阵。该脚本工作在类unix环境中（例如，LINUX, MacOS, Windows Subsystem for LINUX）。BAD2matrix有助于简化系统基因组学管道，可以在GNU通用公共许可证v2下从https://github.com/dpl10/BAD2matrix/tree/master下载。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

查看原文本刊更多论文

BAD2matrix: Phylogenomic matrix concatenation, indel coding, and more

Premise

Common steps in phylogenomic matrix production include biological sequence concatenation, morphological data concatenation, insertion/deletion (indel) coding, gene content (presence/absence) coding, removing uninformative characters for parsimony analysis, recording with reduced amino acid alphabets, and occupancy filtering. Existing software does not accomplish these tasks on a phylogenomic scale using a single program.

Methods and Results

BAD2matrix is a Python script that performs the above-mentioned steps in phylogenomic matrix construction for DNA or amino acid sequences as well as morphological data. The script works in UNIX-like environments (e.g., LINUX, MacOS, Windows Subsystem for LINUX).

Conclusions

BAD2matrix helps simplify phylogenomic pipelines and can be downloaded from https://github.com/dpl10/BAD2matrix/tree/master under a GNU General Public License v2.

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

Applications in Plant Sciences PLANT SCIENCES-

CiteScore

7.30

自引率

0.00%

发文量

审稿时长

12 weeks

期刊介绍： Applications in Plant Sciences (APPS) is a monthly, peer-reviewed, open access journal promoting the rapid dissemination of newly developed, innovative tools and protocols in all areas of the plant sciences, including genetics, structure, function, development, evolution, systematics, and ecology. Given the rapid progress today in technology and its application in the plant sciences, the goal of APPS is to foster communication within the plant science community to advance scientific research. APPS is a publication of the Botanical Society of America, originating in 2009 as the American Journal of Botany''s online-only section, AJB Primer Notes & Protocols in the Plant Sciences. APPS publishes the following types of articles: (1) Protocol Notes describe new methods and technological advancements; (2) Genomic Resources Articles characterize the development and demonstrate the usefulness of newly developed genomic resources, including transcriptomes; (3) Software Notes detail new software applications; (4) Application Articles illustrate the application of a new protocol, method, or software application within the context of a larger study; (5) Review Articles evaluate available techniques, methods, or protocols; (6) Primer Notes report novel genetic markers with evidence of wide applicability.