IQtree笔记

根据windows软件phylosuite跑的IQtree代码，修改后在服务器中跑
phylosuite原代码

Command: D:\software\PhyloSuite_v1.2.2_Win64_with_plugins\PhyloSuite_v1.2.2_Win\PhyloSuite\plugins\iqtree-1.6.8-Windows\bin\iqtree.exe -s D:/software/PhyloSuite_v1.2.2_Win64_with_plugins/PhyloSuite_v1.2.2_Win/PhyloSuite/myWorkPlace/GenBank_File/files\IQtree_results\accD_mafft\accD_mafft.fas -st CODON11 -m TEST -alrt 1000 -bb 5000 -bcor 0.90 -wbt -nt AUTO

修改后代码

Command: bin\iqtree.exe -s accD_mafft.fas -st CODON11 -m MFP -alrt 1000 -bb 5000 -bcor 0.90 -T AUTO -wbt

代码说明

-m MFP（版本1.5.4之后，且为默认参数）和 -m TESTNEW（版本1.5.3之前）是不同版本的同义代码

20201218日更新代码：IQtree批量建树

/root/anaconda3/bin/iqtree -s /home/xmz/data/IQtree/单个基因分别建树 -st CODON11 -m MFP -alrt 1000 -bb 5000 -bcor 0.90 -T AUTO -wbt

图片.png

-alrt SH-aLRT检验，检验树的拓扑结构可信度，作者推荐大数据运算时使用。

The branches of the resulting .treefile will be assigned with both SH-aLRT and
UFBoot support values, which are readable by any tree viewer program like FigTree,
Dendroscope or ETE. You can also look at the textual tree fgure in .iqtree fle:
TIP: Starting with version 1.5.4, -m MFP is the default behavior. Thus, this run is equivalent to iqtree -s example.phy.