多序列比对
# 蛋白序列多重比较构建进化树## Phylogenetic analyses of NLRs
The polypeptide sequences of various disease resistance genes from Triticum spp. and related genera were aligned using Muscle v5.1 software. The sequences were assembled to form a Maximum-likehood phylogenetic tree tested by bootstrapping (1000 replications) using FastTree v2.1.11 software. Phylogenetic trees were further processed and visualized using FigTree and iTOL.
### muscle多重比较
```shell
muscle -align sequence.pep -output sequence.pep.muscle
```
### trimal修剪
```shell
trimal -insequence.pep.muscle -out sequence.pep.muscle.trimal -automated1
```
### FastTree建树
```shell
FastTree sequence.pep.muscle.trimal > sequence.pep.muscle.trimal.tree
```
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