爱华网jackknifed_beta_diversity.py
-i 输入文件， otu_table.biom
-o 输出文件夹
-e 每个样品抽取的序列数
-m Mapping文件
-t 进化树文件
-p 参数文件，用来改变默认的输出
--master_tree mastertree的来源，“consensus”（默认的）来自jackknifedotu tables，“full”来自为取样的otutable
-f 覆盖已有同样名字的文件件
-w 显示命令，但不调用他们，用来排错
-a 平行运行
-O Number of jobs to start. NOTE: youmust also pass -a to run in parallel, this defines the number ofjobs to be started if and only if -a is passed [default:2]
jackknifed_beta_diversity.py-iotu_table/otu_table.biom -t rep_phylo.tre -m map.txt -odiv_jack/ -e 3703
生成了一个log_20140619114438.txt文件，里面详细记载了调用的脚本，详解如下。
1，Beta多样性分析，计算weighted_unifrac,unweighted_unifrac距离
python /usr/lib/qiime/bin//beta_diversity.py -iotu_table/otu_table.biom -o div_jack/ -trep_phylo.tre
2，根据e值重新取样，10次
python /usr/lib/qiime/bin//multiple_rarefactions_even_depth.py-i otu_table/otu_table.biom -d 3703 -odiv_jack//rarefaction/
3，UPGMA构建进化树
# UPGMA on full distance matrix: weighted_unifraccommand
python /usr/lib/qiime/bin//upgma_cluster.py-i div_jack//weighted_unifrac_otu_table.txt -odiv_jack//weighted_unifrac//otu_table_upgma.tre
利用没有随即取样的Otu.biom建立的样品距离矩阵，upgma利用这个距离矩阵来建立进化树。
4，重新取样的Otu计算距离矩阵
# Beta diversity on rarefied OTU tables (weighted_unifrac)command
python /usr/lib/qiime/bin//beta_diversity.py -idiv_jack//rarefaction/ -odiv_jack//weighted_unifrac//rare_dm/ -mweighted_unifrac -t rep_phylo.tre
对随即取样后的10个生成文件，计算其每个文件中样品的距离
5，重新取样的Out, UPGMA构建进化树
# UPGMA on rarefied distance matrix (weighted_unifrac)command
python /usr/lib/qiime/bin//upgma_cluster.py -idiv_jack//weighted_unifrac//rare_dm/ -odiv_jack//weighted_unifrac//rare_upgma/
对上面的文件的距离矩阵，利用upgma构建进化树。
6, 重新取样的Out, UPGMA构建的10个进化树获得一致性的一个进化树
# consensus on rarefied distance matrices(weighted_unifrac) command
python /usr/lib/qiime/bin//consensus_tree.py -idiv_jack//weighted_unifrac//rare_upgma/ -odiv_jack//weighted_unifrac//rare_upgma_consensus.tre
7，树的比较：10个树跟获得的一致性的树比较
# Tree compare (weighted_unifrac) command
python/usr/lib/qiime/bin//tree_compare.py -sdiv_jack//weighted_unifrac//rare_upgma/ -mdiv_jack//weighted_unifrac//rare_upgma_consensus.tre -odiv_jack//weighted_unifrac//upgma_cmp/
8，对10次抽样的距离矩阵做pcoa分析
# Principal coordinates (weighted_unifrac)command
python /usr/lib/qiime/bin//principal_coordinates.py-i div_jack//weighted_unifrac//rare_dm/ -odiv_jack//weighted_unifrac//pcoa/
9，pcoa分析后的2D作图，
# 2d plots (weighted_unifrac) command
python /usr/lib/qiime/bin//make_2d_plots.py -idiv_jack//weighted_unifrac//pcoa/ -odiv_jack//weighted_unifrac//2d_plots/ -m map.txt
这一步产生了4组图？为什么10个样，只有这四个图，是否之间有什么联系呢？
这4组图貌似就颜色就一样，但是他选择的是哪个矩阵呢？
10，pcoa分析后的3D作图，
# 3d plots (weighted_unifrac) command
python /usr/lib/qiime/bin//make_3d_plots.py -idiv_jack//weighted_unifrac//pcoa/ -odiv_jack//weighted_unifrac//3d_plots/ -m map.txt
11，unweighted分析
#UPGMA on full distance matrix: unweighted_unifraccommand
python /usr/lib/qiime/bin//upgma_cluster.py -idiv_jack//unweighted_unifrac_otu_table.txt -odiv_jack//unweighted_unifrac//otu_table_upgma.tre
#Beta diversity on rarefied OTU tables (unweighted_unifrac)command
python /usr/lib/qiime/bin//beta_diversity.py -idiv_jack//rarefaction/ -odiv_jack//unweighted_unifrac//rare_dm/ -munweighted_unifrac -t rep_phylo.tre
#UPGMA on rarefied distance matrix (unweighted_unifrac)command
python /usr/lib/qiime/bin//upgma_cluster.py -idiv_jack//unweighted_unifrac//rare_dm/ -odiv_jack//unweighted_unifrac//rare_upgma/
#consensus on rarefied distance matrices (unweighted_unifrac)command
python /usr/lib/qiime/bin//consensus_tree.py -idiv_jack//unweighted_unifrac//rare_upgma/ -odiv_jack//unweighted_unifrac//rare_upgma_consensus.tre
#Tree compare (unweighted_unifrac) command
python /usr/lib/qiime/bin//tree_compare.py -sdiv_jack//unweighted_unifrac//rare_upgma/ -mdiv_jack//unweighted_unifrac//rare_upgma_consensus.tre -odiv_jack//unweighted_unifrac//upgma_cmp/
#Principal coordinates (unweighted_unifrac) command
python /usr/lib/qiime/bin//principal_coordinates.py -idiv_jack//unweighted_unifrac//rare_dm/ -odiv_jack//unweighted_unifrac//pcoa/
# 2dplots (unweighted_unifrac) command
python /usr/lib/qiime/bin//make_2d_plots.py -idiv_jack//unweighted_unifrac//pcoa/ -odiv_jack//unweighted_unifrac//2d_plots/ -m map.txt
# 3dplots (unweighted_unifrac) command
python /usr/lib/qiime/bin//make_3d_plots.py -idiv_jack//unweighted_unifrac//pcoa/ -odiv_jack//unweighted_unifrac//3d_plots/ -m map.txt
参考资料：
http://qiime.org/scripts/jackknifed_beta_diversity.html
