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
mkdir output
/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
itol导出svg修改" width="860" height="950" viewBox="0,30,860,950">