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（一）利用ncbi-genome-download批量下载基因组文件12#安装conda install bioconda::ncbi-genome-download
主要参数groups参数定于目标物种所在的大类，包括’all’, ‘archaea’, ‘bacteria’, ‘fungi’, ‘invertebrate’, ‘metagenomes’, ‘plant’, ‘protozoa’, ‘vertebrate_mammalian’, ‘vertebrate_other’, ‘viral’。只将所属类群的名字放在命令行中-s或–section 选择数据库refseq或genbank，一般不添加该参数，默认为refseq数据库-t或–taxid 添加所下载物种在ncbi的id，可以直接添加，也可以放入一个文件中批量下载多个物种-F或–formats 定义所需物种的数据的类型，包括’genbank’, ‘fasta’, ‘rm’, ‘features’, ‘gff’, ‘p ...</div></div></div><div class="recent-post-item"><div class="recent-post-info no-cover"><a class="article-title" href="/2024/07/17/genome-anno/" title="基因组注释——适合初学者的流程分解版">基因组注释——适合初学者的流程分解版</a><div class="article-meta-wrap"><span class="post-meta-date"><i class="far fa-calendar-alt"></i><span class="article-meta-label">发表于</span><time datetime="2024-07-17T13:06:54.000Z" title="发表于 2024-07-17 21:06:54">2024-07-17</time></span></div><div class="content">主题：基因组注释相关参考：
基因组注释（一）：重复序列注释 | 生信技工 (yanzhongsino.github.io)
使用RepeatModeler从头预测基因组重复序列 | BioChen 博客
【基因组注释】RepeatMasker和RepeatModeler安装、配置与运行避坑 - 简书 (jianshu.com)
基因组重复序列注释repeatmask&repeatmodeler - 知乎 (zhihu.com)
非模式生物重复序列注释 RepeatModeler2+RepeatMasker4 - 简书 (jianshu.com)
基因组注释（2）——散在重复序列注释 - 我的小破站 (phantom-aria.github.io)
使用AUGSTUS+Geneid+GeneMark+GeMoMa+GenomeThreader+Exonerate进行基因结构预测 - 知乎 (zhihu.com)
基因组结构注释软件列表 - 简书 (jianshu.com)
基因组注释（1）——串联重复序列注释 - 我的小破站 (phantom-aria.github.io)
1 ...</div></div></div><div class="recent-post-item"><div class="post_cover left"><a href="/2024/04/09/QuIBL%E6%96%B9%E6%B3%95%E6%A3%80%E9%AA%8C%E5%9F%BA%E5%9B%A0%E6%B8%90%E6%B8%97%E5%92%8C%E4%B8%8D%E5%AE%8C%E5%85%A8%E8%B0%B1%E7%B3%BB%E5%88%86%E9%80%89/" title="QuIBL方法检验基因渐渗和不完全谱系分选"><img class="post-bg" src="/2024/04/09/QuIBL%E6%96%B9%E6%B3%95%E6%A3%80%E9%AA%8C%E5%9F%BA%E5%9B%A0%E6%B8%90%E6%B8%97%E5%92%8C%E4%B8%8D%E5%AE%8C%E5%85%A8%E8%B0%B1%E7%B3%BB%E5%88%86%E9%80%89/2024-04-09%20154337.png" onerror="this.onerror=null;this.src='/img/404.jpg'" alt="QuIBL方法检验基因渐渗和不完全谱系分选"></a></div><div class="recent-post-info"><a class="article-title" href="/2024/04/09/QuIBL%E6%96%B9%E6%B3%95%E6%A3%80%E9%AA%8C%E5%9F%BA%E5%9B%A0%E6%B8%90%E6%B8%97%E5%92%8C%E4%B8%8D%E5%AE%8C%E5%85%A8%E8%B0%B1%E7%B3%BB%E5%88%86%E9%80%89/" title="QuIBL方法检验基因渐渗和不完全谱系分选">QuIBL方法检验基因渐渗和不完全谱系分选</a><div class="article-meta-wrap"><span class="post-meta-date"><i class="far fa-calendar-alt"></i><span class="article-meta-label">发表于</span><time datetime="2024-04-09T07:30:28.000Z" title="发表于 2024-04-09 15:30:28">2024-04-09</time></span><span class="article-meta"><span class="article-meta-separator">|</span><i class="fas fa-inbox"></i><a class="article-meta__categories" href="/categories/%E7%BD%91%E7%8A%B6%E8%BF%9B%E5%8C%96/">网状进化</a></span></div><div class="content">QuIBL是2019年science蝴蝶辐射演化分析中检测渐渗的新方法，其用法为python脚本QuIBL.py的使用
1、安装在github下载软件包：https://github.com/miriammiyagi/QuIBL
123wget https://github.com/miriammiyagi/QuIBL/archive/refs/heads/master.zipunzip master.zip
该脚本依赖python2.7，且依赖以下包joblib, ete3, itertools, sys, numpy, math, ConfigParser, csv, and multiprocessing
#创建python2的环境
12conda create -n python2.7 python=2.7conda activate python2.7
#通过运行示例文件来检查不存在的依赖包
1python QuIBL.py ./Small_Test_Example/sampleInputFile.txt
#通过多次运行实例文件的报错，发现te3和joblib是存在问题 ...</div></div></div><div class="recent-post-item"><div class="post_cover right"><a href="/2024/01/20/%E6%BA%AF%E7%A5%96%E6%A0%91%E4%B8%8E%E5%9F%BA%E5%9B%A0%E6%A0%91%E4%B9%8B%E9%97%B4%E5%86%B2%E7%AA%81%E7%9A%84%E5%8F%AF%E8%A7%86%E5%8C%96/" title="溯祖树与基因树之间冲突的可视化"><img class="post-bg" src="/2024/01/20/%E6%BA%AF%E7%A5%96%E6%A0%91%E4%B8%8E%E5%9F%BA%E5%9B%A0%E6%A0%91%E4%B9%8B%E9%97%B4%E5%86%B2%E7%AA%81%E7%9A%84%E5%8F%AF%E8%A7%86%E5%8C%96/1.png" onerror="this.onerror=null;this.src='/img/404.jpg'" alt="溯祖树与基因树之间冲突的可视化"></a></div><div class="recent-post-info"><a class="article-title" href="/2024/01/20/%E6%BA%AF%E7%A5%96%E6%A0%91%E4%B8%8E%E5%9F%BA%E5%9B%A0%E6%A0%91%E4%B9%8B%E9%97%B4%E5%86%B2%E7%AA%81%E7%9A%84%E5%8F%AF%E8%A7%86%E5%8C%96/" title="溯祖树与基因树之间冲突的可视化">溯祖树与基因树之间冲突的可视化</a><div class="article-meta-wrap"><span class="post-meta-date"><i class="far fa-calendar-alt"></i><span class="article-meta-label">发表于</span><time datetime="2024-01-20T11:21:18.000Z" title="发表于 2024-01-20 19:21:18">2024-01-20</time></span><span class="article-meta"><span class="article-meta-separator">|</span><i class="fas fa-inbox"></i><a class="article-meta__categories" href="/categories/%E7%BD%91%E7%8A%B6%E8%BF%9B%E5%8C%96/">网状进化</a></span></div><div class="content">溯祖树与基因树之间冲突的可视化主要用到PhyParts软件以及phypartspiecharts.py脚本
参考网站：
blackrim / phyparts / README.md — Bitbucket
phyloscripts/phypartspiecharts at master · mossmatters/phyloscripts · GitHub
Abronia HybSeq Phylogeny - HackMD
以上的英文页面讲解非常清晰，在此抛砖引玉，方便大家检索。
一、phyparts的安装（首先保证运行环境有maven，否则无法安装）1234567891011git clone https://bitbucket.org/blackrim/phyparts.gitsh mvn_cmdline.sh（安装失败）##缺少依赖，安装mavenconda install conda-forge::mavensh mvn_cmdline.sh（安装成功）java -jar target/phyparts-0.0.1-SNAPSHOT-j ...</div></div></div><div class="recent-post-item"><div class="post_cover left"><a href="/2023/10/07/phylonetwork/" title="系统发育网络推断软件PhyloNetworks和Phylonet的使用及遇到的error"><img class="post-bg" src="/2023/10/07/phylonetwork/1.png" onerror="this.onerror=null;this.src='/img/404.jpg'" alt="系统发育网络推断软件PhyloNetworks和Phylonet的使用及遇到的error"></a></div><div class="recent-post-info"><a class="article-title" href="/2023/10/07/phylonetwork/" title="系统发育网络推断软件PhyloNetworks和Phylonet的使用及遇到的error">系统发育网络推断软件PhyloNetworks和Phylonet的使用及遇到的error</a><div class="article-meta-wrap"><span class="post-meta-date"><i class="far fa-calendar-alt"></i><span class="article-meta-label">发表于</span><time datetime="2023-10-07T08:07:46.000Z" title="发表于 2023-10-07 16:07:46">2023-10-07</time></span><span class="article-meta"><span class="article-meta-separator">|</span><i class="fas fa-inbox"></i><a class="article-meta__categories" href="/categories/%E7%BD%91%E7%8A%B6%E8%BF%9B%E5%8C%96/">网状进化</a></span></div><div class="content">一、系统发育网络推断软件PhyloNetworks的使用流程以及解决报错该软件的详细说明请参考他的官方网站Home · PhyloNetworks.jl (crsl4.github.io)，该软件的中文流程（包括简介、安装使用流程等）请参考系统发育网络推断 —— PhyloNetworks | 生信技工 (yanzhongsino.github.io)，本笔记参考以上两个站点并测试无报错。
1、安装12345678wget https://julialang-s3.julialang.org/bin/linux/x64/1.7/julia-1.7.2-linux-x86_64.tar.gz #下载tar -xzf julia-1.7.2-linux-x86_64.tar.gz #解压julia-1.7.2/bin/julia -h #若无报错则安装julia成功julia-1.7.2/bin/julia #进入julia运行界面，类似于python和r的交互模式julia> using Pkg #类似于r的library和python的import来加载函数julia> ...</div></div></div><div class="recent-post-item"><div class="recent-post-info no-cover"><a class="article-title" href="/2023/10/05/%E5%88%A9%E7%94%A8ete3%E6%89%B9%E9%87%8F%E5%AF%B9%E5%9F%BA%E5%9B%A0%E6%A0%91%E5%AE%9A%E6%A0%B9/" title="利用ete3批量对基因树定根并检测单系性">利用ete3批量对基因树定根并检测单系性</a><div class="article-meta-wrap"><span class="post-meta-date"><i class="far fa-calendar-alt"></i><span class="article-meta-label">发表于</span><time datetime="2023-10-05T13:48:42.000Z" title="发表于 2023-10-05 21:48:42">2023-10-05</time></span><span class="article-meta"><span class="article-meta-separator">|</span><i class="fas fa-inbox"></i><a class="article-meta__categories" href="/categories/%E6%89%B9%E9%87%8F%E5%A4%84%E7%90%86%E6%96%B9%E6%B3%95/">批量处理方法</a></span></div><div class="content">利用ete3的set_outgroup函数批量对基因树定根并利用check_monophyly函数检测单系性对溯祖法得到的多个基因树进行定根，将多个基因树文件cat到一个文件中，得到alltree.txt，利用以下脚本对其批量定根。12345678910111213###首先下载ete3工具包from ete3 import Treefor i in range(7121): #提前创建7122个文件，用于写入定根后的树文件，修改为基因的数量减一 f = open('./%s'%i + '.txt',"a") f.write("")n=0with open('alltree.txt','r') as f: for line in f: t = Tree(line) t.set_outgroup(t&"mcap") #设置 ...</div></div></div><div class="recent-post-item"><div class="post_cover left"><a href="/2023/09/02/%E5%88%A9%E7%94%A8cafe5%E8%BF%9B%E8%A1%8C%E5%9F%BA%E5%9B%A0%E5%AE%B6%E6%97%8F%E6%89%A9%E5%BC%A0%E6%94%B6%E7%BC%A9%E5%88%86%E6%9E%90/" title="利用cafe5进行基因家族扩张收缩分析"><img class="post-bg" src="/2023/09/02/%E5%88%A9%E7%94%A8cafe5%E8%BF%9B%E8%A1%8C%E5%9F%BA%E5%9B%A0%E5%AE%B6%E6%97%8F%E6%89%A9%E5%BC%A0%E6%94%B6%E7%BC%A9%E5%88%86%E6%9E%90/1.jpg" onerror="this.onerror=null;this.src='/img/404.jpg'" alt="利用cafe5进行基因家族扩张收缩分析"></a></div><div class="recent-post-info"><a class="article-title" href="/2023/09/02/%E5%88%A9%E7%94%A8cafe5%E8%BF%9B%E8%A1%8C%E5%9F%BA%E5%9B%A0%E5%AE%B6%E6%97%8F%E6%89%A9%E5%BC%A0%E6%94%B6%E7%BC%A9%E5%88%86%E6%9E%90/" title="利用cafe5进行基因家族扩张收缩分析">利用cafe5进行基因家族扩张收缩分析</a><div class="article-meta-wrap"><span class="post-meta-date"><i class="far fa-calendar-alt"></i><span class="article-meta-label">发表于</span><time datetime="2023-09-02T10:33:56.000Z" title="发表于 2023-09-02 18:33:56">2023-09-02</time></span><span class="article-meta"><span class="article-meta-separator">|</span><i class="fas fa-inbox"></i><a class="article-meta__categories" href="/categories/%E5%88%86%E6%9E%90%E7%AC%94%E8%AE%B0/">分析笔记</a></span></div><div class="content">利用cafe5进行基因家族扩张收缩分析测试于2023年9月1日
基于orthofinder直系同源聚类的结果，可以看在树的特定节点上哪些基因家族发生了扩张与收缩
软件安装
123456#在单独的conda环境里安装并运行，避免环境冲突conda activate biosoftconda install -c bioconda cafe#测试成功安装cafe5 -h
准备文件包括1、带有分歧时间的树，由MCMCtree产生；2、直系同源基因家族的聚类情况，由orthofinder结果产生；
123456789101112131415#step 1 准备树文件，FigTree.tre来自MCMCtree结果grep "UTREE 1 =" FigTree.tre | sed -E -e "s/\[[^]]*\]//g" -e "s/[ \t]//g" -e "/^$/d" -e "s/UTREE1=//" > tree.txt#step 2 用orthofinder2 ...</div></div></div><div class="recent-post-item"><div class="recent-post-info no-cover"><a class="article-title" href="/2023/04/04/ete3/" title="ete3">ete3</a><div class="article-meta-wrap"><span class="post-meta-date"><i class="far fa-calendar-alt"></i><span class="article-meta-label">发表于</span><time datetime="2023-04-04T01:33:35.000Z" title="发表于 2023-04-04 09:33:35">2023-04-04</time></span></div><div class="content">如何利用ete3包从系统发育树中提取子树ete3：用于构建、比较、注释、操作和可视化系统发育树的Python包。
12345678conda install ete3 #conda安装python #在操作文件目录下进入python命令行交互界面import ete3 #导入ete3包t = ete3.Tree("tree.txt") #将原来的进化树定义为tsubtree_taxa = ["Orbicella_annularis","Pocillipora_damicornis","Stylophora_pistillata","Hydra_vulgaris","Acropora_digitifera","Acropora_millepora","Acropora_tenuis","Porites_lutea","Renilla_muelleri","Discosoma ...</div></div></div><div class="recent-post-item"><div class="post_cover left"><a href="/2022/12/17/learn-perl/" title="learn_perl"><img class="post-bg" src="/2022/12/17/learn-perl/perl.jpg" onerror="this.onerror=null;this.src='/img/404.jpg'" alt="learn_perl"></a></div><div class="recent-post-info"><a class="article-title" href="/2022/12/17/learn-perl/" title="learn_perl">learn_perl</a><div class="article-meta-wrap"><span class="post-meta-date"><i class="far fa-calendar-alt"></i><span class="article-meta-label">发表于</span><time datetime="2022-12-17T11:04:21.000Z" title="发表于 2022-12-17 19:04:21">2022-12-17</time></span></div><div class="content">Perl是一种高效处理文本文件的脚本语言，下面记录了一些常用的基因序列处理的perl函数或工具
数据类型1、scalar大小写转换工具：
1234uc $seq_of_BRAC2; #转大写lc $seq_of_BRAC2; #转小写$seq_of_BRAC2 =~ tr/atgc/ATGC/; #转大写$seq_of_BRAC2 =~ tr/ATGC/atgc/; #转小写
利用tr工具统计4种碱基的个数
123my $count = $seperate_dna =~ tr/atgc/atgc/; #统计$seperate_dna中小写atgc的数目my $count = $seperate_dna =~ tr/ATGC/ATGC/; #统计$seperate_dna中大写ATGC的数目my $count = $seperate_dna =~ tr/A/A/; #统计$seperate_dna中A的数目
取反向互补序列
12my $reversed_zika_DNA = reverse($zika_DNA);$reversed_zika_DNA =~ tr/ATC ...</div></div></div><div class="recent-post-item"><div class="recent-post-info no-cover"><a class="article-title" href="/2022/09/24/3%E7%A7%8Dlinux%E4%B8%8B%E6%8F%90%E5%8F%96%E4%B8%A4%E4%B8%AA%E6%96%87%E4%BB%B6%E7%9A%84%E4%B8%8D%E5%90%8C%E8%A1%8C%E5%86%85%E5%AE%B9%E7%9A%84%E6%96%B9%E6%B3%95/" title="提取两文件的不同行">提取两文件的不同行</a><div class="article-meta-wrap"><span class="post-meta-date"><i class="far fa-calendar-alt"></i><span class="article-meta-label">发表于</span><time datetime="2022-09-24T05:16:38.000Z" title="发表于 2022-09-24 13:16:38">2022-09-24</time></span></div><div class="content">文件的情景：prank.sh.completed是prank.sh的子集：
123cat prank.sh prank.sh.completed | sort | uniq -d >temp.txtcat prank.sh temp.txt | sort | uniq -u > different.txt
（以下内容搭个便车）
前两天，利用cafe4.2的版本分析，根据本地以及网上教程，
在网上下载了各种现成的脚本，真方便。
1cafe 01cafe.sh
上述命令运行报错（忘了记录）。原因：缺少树的祖先位置的λ分类。添加即可。
在提取扩张收缩的基因家族ID时，cafetutorial_report_analysis.py脚本运行报错（忘了记录）。原因：缺少cafecore moduel。解决方法：github上搜索并下载cafecore.py，添加到python脚本目录下。
运行时又有了以下报错
123File "./cafecore.py", line 8<!DOCTYPE html>^SyntaxError: invalid ...</div></div></div><nav id="pagination"><div class="pagination"><span class="page-number current">1</span><a class="page-number" href="/page/2/#content-inner">2</a><a class="page-number" href="/page/3/#content-inner">3</a><a class="extend next" rel="next" href="/page/2/#content-inner"><i class="fas fa-chevron-right fa-fw"></i></a></div></nav></div><div class="aside-content" id="aside-content"><div class="card-widget card-info"><div class="is-center"><div class="avatar-img"><img src="/img/orca-295051_1280.png" onerror="this.onerror=null;this.src='/img/friend_404.gif'" alt="avatar"/></div><div class="author-info__name">吴 田 振</div><div class="author-info__description">努力发一区</div></div><div class="card-info-data site-data is-center"><a href="/archives/"><div class="headline">文章</div><div class="length-num">30</div></a><a href="/tags/"><div class="headline">标签</div><div class="length-num">19</div></a><a 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