RdhA蛋白序列发育树构建及iTol美化 |
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构建96characteristic rdhA和8E 8P ZNEPE的系统发育树
将蛋白序列保存在gigys服务器中：/data/ys202108/genedata/phylogeny/proteinTreeData/TreeOfBinZNE71Bin8E40Bin8P27BinZNP1BinZNV4And96CharactericRhdA/FunctionalRdhAFromElizabethORFsinRdhAmetabat.ZNE71-8E40-8P27-ZNP1-ZNV4.protein.faa #登录gigys服务器 #激活conda环境 conda activate phylo #对齐 mafft --maxiterate 1000 --localpair FunctionalRdhAFromElizabethORFsinRdhAmetabat.ZNE71-8E40-8P27-ZNP1-ZNV4.protein.faa > mafft.faa #剪切 trimal -in mafft.faa -out trimal.faa -gappyout -fasta #构树 /data/ys202108/genedata/phylogeny/RAxML/standard-RAxML-master/raxmlHPC-PTHREADS-AVX -s trimal.faa -n RAxML -w /data/ys202108/genedata/phylogeny/proteinTreeData/TreeOfBinZNE71Bin8E40Bin8P27BinZNP1BinZNV4And96CharactericRhdA/output -N 1000 -m PROTGAMMAILGX -T 80 -f a -p 12345 -x 12345 #结果 Program execution info written to /data/ys202108/genedata/phylogeny/proteinTreeData/TreeOfBinZNE71Bin8E40Bin8P27BinZNP1BinZNV4And96CharactericRhdA/output/RAxML_info.RAxML All 1000 bootstrapped trees written to: /data/ys202108/genedata/phylogeny/proteinTreeData/TreeOfBinZNE71Bin8E40Bin8P27BinZNP1BinZNV4And96CharactericRhdA/output/RAxML_bootstrap.RAxML Best-scoring ML tree written to: /data/ys202108/genedata/phylogeny/proteinTreeData/TreeOfBinZNE71Bin8E40Bin8P27BinZNP1BinZNV4And96CharactericRhdA/output/RAxML_bestTree.RAxML Best-scoring ML tree with support values written to: /data/ys202108/genedata/phylogeny/proteinTreeData/TreeOfBinZNE71Bin8E40Bin8P27BinZNP1BinZNV4And96CharactericRhdA/output/RAxML_bipartitions.RAxML Best-scoring ML tree with support values as branch labels written to: /data/ys202108/genedata/phylogeny/proteinTreeData/TreeOfBinZNE71Bin8E40Bin8P27BinZNP1BinZNV4And96CharactericRhdA/output/RAxML_bipartitionsBranchLabels.RAxML #以RAxML_bipartitionsBranchLabels.RAxML为输出 iTOL美化 登录iTol 导入：RAxML_bipartitionsBranchLabels.RAxML Re-root: NA2 RS14425 Scaling factors: 0.5 >修改tree的基因名称 将E:\Gene\GZZN\美格 GZZN-IP_LZmedium_ISO32&V_LZmedium_ISO24 Meta\宏基因组分析流程\ZNPVdehalcoccoideBin发育树\RdhA发育树中的RdhAlabels_template.txt拉入itol |
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