Mafft Trimal Fasttree序列对齐修剪建树

导读

barrnap预测细菌基因组16S，获取结果文件第二行最长16S，保留>1400bp的16S。mafft做序列对齐。trimal修剪序列。fasttree建树。ggtree可视化。figtree也可简要查看tree文件。下面从整理好的16S序列文件开始。

1 准备输入文件

2 mafft 对齐序列

windows版本：https://www.jianshu.com/p/d61cf5861e65

mafft --auto bgi_illumina_16S.fa > bgi_illumina_16S_align.fa

3 trimal 修剪

官网：http://trimal.cgenomics.org/
下载：http://trimal.cgenomics.org/downloads
手册：http://trimal.cgenomics.org/getting_started_with_trimal_v1.2

trimal \
-in bgi_illumina_16S_align.fa \
-out bgi_illumina_16S_align_filter.fa \
-automated1
# Use a heuristic selection of the automatic method based on similarity statistics. (see User Guide). (Optimized for Maximum Likelihood phylogenetic tree reconstruction).

4 fasttree建树

官网？：https://bioinformaticsworkbook.org/phylogenetics/FastTree.html#gsc.tab=0
官网？工作流：sequences -> MAFFT -> FastTree -> FigTree -> pdf

fasttree \
-nt bgi_illumina_16S_align_filter.fa \
> bgi_illumina_16S_align_filter.tree

5 ggtree 可视化

library("ggplot2")
library("ggtree")
data = read.tree("bgi_illumina_16S_align_filter.tree")
tree = fortify(data)

gra3 = 
ggtree(data, layout="fan", branch.length="none", size=0.8) %<+% pal +
geom_tiplab(aes(label = mark, col = Platform),  
            size=3) +
scale_color_manual(
    values = c("BGI" = "orangered3", 
               "Illumina" = "deepskyblue3"))

ggsave(gra3, file="tree3.jpg")

iqtree建树

mafft --auto Tree.fas > Tree.fas.mafft
iqtree -s Tree.fas.mafft -m MFP -bb 1000 -bnni -redo -o NC_010433

植物叶绿体基因组--组装，注释和比较作图