前面写了16S rDNA进化树。关于细菌基因组水平，下面记录这篇文章用了三种不同的流程reconstruct phylogenetic structure的策略。

标题：Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle
杂志：CELL
时间：2019

策略一（Figure 1）

PhyloPhlAn软件
400 universal PhyloPhlAn markers构建phylogeny
phylophlan参数：--diversity high --accurate --min_num_markers 80

Internal steps:
diamond：
blastx --quiet --threads 1 --outfmt 6 --more-sensitive --id 50 --max-hsps 35 -k 0
diamond:
blastp --quiet --threads 1 --outfmt 6 --more-sensitive --id 50 --max-hsps 35 -k 0
mafft --anysymbol 对齐
trimal -gappyout 修剪
RAxML -m PROTCATLG -p 1989 建树

策略二（Figure S3）

PhyloPhlAn软件
400 PhyloPhlAn markers reconstruct phylogeny
phylophlan参数：--diversity high --fast --min_num_markers 80

Internal steps:
diamond：
blastx --quiet --threads 1 --outfmt 6 --more-sensitive --id 50 --max-hsps 35 -k 0
diamond:
blastp --quiet --threads 1 --outfmt 6 --more-sensitive --id 50 --max-hsps 35 -k 0
mafft --anysymbol 对齐
trimal -gappyout 修剪
RAxML -m PROTCATLG -p 1989 建树

IQ-TREE -nt AUTO -m LG 建树

策略三（Figure 3）

Roary identified set of cores genes at 95%

roary -e -n -v -p 4 -i 95 \
-f ./result_roary/ \
./out/*.gff

PhyloPhlAn --diversity low --fast
--min_num_markers <50% of the number of core genes identified>
--min_num_entries <90% of the number of input genomes>

--diversity {low,medium,high}
                        Specify the expected diversity of the phylogeny,
                        automatically adjust some parameters: "low": for
                        genus-/species-/strain-level phylogenies; "medium":
                        for class-/order-level phylogenies; "high": for
                        phylum-/tree-of-life size phylogenies (default: None)
--fast                Perform more a faster phylogeny reconstruction by
                        reducing the phylogenetic positions to use; affected
                        parameters depend on the "--diversity" level (default:
                        False)
--min_num_markers MIN_NUM_MARKERS
                        Input genomes or proteomes that map to less than the
                        specified number of markers will be discarded
                        (default: 1)
--min_num_entries MIN_NUM_ENTRIES
                        The minimum number of entries to be present for each
                        of the markers in the database (default: 4)

blastn -outfmt 6 -max_target_seqs 1000000
mafft --anysymbol --auto 对齐
trimal -gappyout 修剪
FastTree -mlacc 2 -slownni -spr 4 -fastest -mlnni 4 -no2nd -gtr -nt 建树
RAxML -p 1989 -m GTRCAT
-t <phylogenetic tree computed by FastTree>

NMDS基于 Roary 遗传距离

The non-metric multidimensional scaling plots were computed on pairwise genetic distances between core gene alignments produced by Roary using the nmds function in the ecodist R package

可视化

The phylogenetic trees were generated using GraPhlAn and the phylogenies were generated using FigTree

还有更多的方法

文章：Insights on the Evolutionary Genomics of the Blautia Genus: Potential New Species and Genetic Content Among Lineages
杂志：Frontiers in Microbiology
时间：2021

策略四

OrthoFinder获取conserved gene families (Orthogroups)
perl retrieve protein sequence
MAFFT (L-INS-i mode)对齐Orthogroups
ModelTest-NG:
Akaike information criterion (AIC)
IQ-TREE 2:
1000 replicates of ultrafast bootstrap
UFBOOT trees by NNI (–bnni)
SH-like approximate likelihood ratio test (–alrt)

策略五

panX core genome to construct single nucleotide polymorphism (SNP)-based tree
cophylo比较phylogenomic aminoacid and the SNP-based trees

TypeMat from the Microbial Genomes Atlas (MiGA) 进行细菌分类剔除anomalous classification