Beta多样性

• Venn图分析
• 样本聚类树
• PCA分析
• PCoA分析
• NMDS分析
• ADONIS分析
• 群落构建机制分析

otus.fa

>ASV_1
GTAGTCCACGCCGTAAACGGTGGGCGCTAGATGTGGGGACCTTCCACGGTTTCTGCGTCGCAGCTAACGCATTAAGCGCC
CCGCCTGGGGAGTACGGTCGCAAGACTAAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGCGGAGCATGTTGCTTA
ATTCGACGCAACGCGAAGAACCTTACCAAGGCTTGACATCGCCGGAAAACTCGCAGAGATGCGGGGTCCTTTTGGGCCGG
TGACAGGTGGTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTCGTTCT
ATGTTGCCAGCACGCCCTTCGGGGTGGTGGGGACTCATAGGAGACTGCCGGGGTCAACTCGGA
>ASV_2
GTAGTCCACGCCCTAAACGATGTCAACTGGTTGTTGGGAGGGTTTCTTCTCAGTAACGTAGCTAACGCGTGAAGTTGACC
GCCTGGGGAGTACGGCCGCAAGGTTGAAACTCAAAGGAATTGACGGGGACCCGCACAAGCGGTGGATGATGTGGTTTAAT
TCGATGCAACGCGAAAAACCTTACCTACCCTTGACATGTCTGGAATCCTGAAGAGATTTGGGAGTGCTCGAAAGAGAGCC
AGAACACAGGTGCTGCATGGCCGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGT
CATTAGTTGCTACGAAAGGGCACTCTAATGAGACTGCCGGTGACAAACCGGA

#结果有多个文件，需要目录
mkdir -p results/beta/
#基于OTU构建进化树 Make OTU tree, 4s
usearch -cluster_agg results/otus.fa -treeout results/otus.tree
#生成5种距离矩阵：bray_curtis, euclidean, jaccard, manhatten, unifrac
usearch -beta_div results/otutab_rare.txt -tree results/otus.tree \
    -filename_prefix results/beta/

results/beta/
├── bray_curtis_binary.sorted.txt
├── bray_curtis_binary.tree
├── bray_curtis_binary.txt
├── bray_curtis.pcoa.label.pdf
├── bray_curtis.pcoa.pdf
├── bray_curtis.sorted.txt
├── bray_curtis.tree
├── bray_curtis.txt
├── euclidean.sorted.txt
├── euclidean.tree
├── euclidean.txt
├── jaccard_binary.sorted.txt
├── jaccard_binary.tree
├── jaccard_binary.txt
├── jaccard.sorted.txt
├── jaccard.tree
├── jaccard.txt
├── manhatten.sorted.txt
├── manhatten.tree
├── manhatten.txt
├── unifrac_binary.sorted.txt
├── unifrac_binary.tree
├── unifrac_binary.txt
├── unifrac.sorted.txt
├── unifrac.tree
└── unifrac.txt