RdhA蛋白序列发育树构建及iTol美化

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已于 2024-07-30 16:01:10 修改

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于 2023-05-22 08:24:54 首次发布

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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
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