導(dǎo)讀
barrnap預(yù)測細(xì)菌基因組16S，獲取結(jié)果文件第二行最長16S，保留>1400bp的16S。mafft做序列對齊。trimal修剪序列。fasttree建樹。ggtree可視化。figtree也可簡要查看tree文件。下面從整理好的16S序列文件開始。
文章
標(biāo)題：MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
期刊：Molecular Biology and Evolution
時間：2013
被引：21366 （谷歌學(xué)術(shù) 2021.11.24）
標(biāo)題：trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses
期刊：Bioinformatics
時間：2009
被引：4662（谷歌學(xué)術(shù) 2021.11.24）
標(biāo)題：FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments
期刊：Plos one
時間：2010
被引：7840（谷歌學(xué)術(shù) 2021.11.24）
介紹
FastTree 是基于最大似然法構(gòu)建進化樹的軟件，它最大的特點就是運行速度快，支持幾百萬條序列的建樹任務(wù)。但是fasttree不支持bootstrap檢驗以及支持的替換模型有限。
官網(wǎng)如下：http://www.microbesonline.org/fasttree/
替換模型選擇:
FastTree 支持核酸和蛋白的進化樹構(gòu)建，對于核酸，可選的替換模型包括以下幾種：JC（Jukes-Cantor）、GTR（generalized time-reversible），默認(rèn)的模型為JC。對于蛋白質(zhì)，可選的替換模型包括以下幾種：JTT (Jones-Taylor-Thornton 1992)、LG(Le and Gascuel 2008)、WAG(Whelan & Goldman 2001) 默認(rèn)的模型為JTT。FastTree要求輸入的多序列比對結(jié)果為FASTA或者Phylip格式。
來自：https://www.omicsclass.com/article/1343
軟件獲取
conda create -n xgene
conda activate xgene
conda install mafft trimal fasttree
Downloading and Extracting Packages
mafft-7.487 | 3.0 MB | ##################################### | 100%
trimal-1.4.1 | 189 KB | ##################################### | 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
1 準(zhǔn)備輸入文件
2 mafft 對齊序列
windows版本：http://www.itdecent.cn/p/d61cf5861e65
mafft --auto bgi_illumina_16S.fa > bgi_illumina_16S_align.fa
過程：
generating a scoring matrix for nucleotide (dist=200)
Making a distance matrix
Constructing a UPGMA tree (efffree=0) ...
Progressive alignment 1/2...
Making a distance matrix from msa..
Constructing a UPGMA tree (efffree=1)
Progressive alignment 2/2...
disttbfast (nuc) Version 7.487
generating a scoring matrix for nucleotide (dist=200)
dndpre (nuc) Version 7.487
generating a scoring matrix for nucleotide (dist=200)
dvtditr (nuc) Version 7.487
結(jié)果：
3 trimal 修剪
官網(wǎng)：http://trimal.cgenomics.org/
下載：http://trimal.cgenomics.org/downloads
手冊：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建樹
官網(wǎng)？：https://bioinformaticsworkbook.org/phylogenetics/FastTree.html#gsc.tab=0
官網(wǎng)？工作流：sequences -> MAFFT -> FastTree -> FigTree -> pdf
fasttree \
-nt bgi_illumina_16S_align_filter.fa \
> bgi_illumina_16S_align_filter.tree
過程：
FastTree Version 2.1.10 Double precision (No SSE3)
Nucleotide distances: Jukes-Cantor Joins: balanced Support: SH-like 1000
Search: Normal +NNI +SPR (2 rounds range 10) +ML-NNI opt-each=1
TopHits: 1.00*sqrtN close=default refresh=0.80
ML Model: Jukes-Cantor, CAT approximation with 20 rate categories
5 ggtree 可視化
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建樹
mafft --auto Tree.fas > Tree.fas.mafft
iqtree -s Tree.fas.mafft -m MFP -bb 1000 -bnni -redo -o NC_010433
