   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_46_5.biom -o arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_46_5.biom -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_46_5.biom arare_max100//alpha_div//alpha_rarefaction_46_5.biom   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_46_6.biom -o arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_46_6.biom -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_46_6.biom arare_max100//alpha_div//alpha_rarefaction_46_6.biom   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_46_7.biom -o arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_46_7.biom -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_46_7.biom arare_max100//alpha_div//alpha_rarefaction_46_7.biom   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_46_8.biom -o arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_46_8.biom -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_46_8.biom arare_max100//alpha_div//alpha_rarefaction_46_8.biom   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_46_9.biom -o arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_46_9.biom -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_46_9.biom arare_max100//alpha_div//alpha_rarefaction_46_9.biom   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_55_0.biom -o arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_55_0.biom -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_55_0.biom arare_max100//alpha_div//alpha_rarefaction_55_0.biom   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_55_1.biom -o arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_55_1.biom -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_55_1.biom arare_max100//alpha_div//alpha_rarefaction_55_1.biom   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_55_2.biom -o arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_55_2.biom -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_55_2.biom arare_max100//alpha_div//alpha_rarefaction_55_2.biom   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_55_3.biom -o arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_55_3.biom -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_55_3.biom arare_max100//alpha_div//alpha_rarefaction_55_3.biom   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_55_4.biom -o arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_55_4.biom -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_55_4.biom arare_max100//alpha_div//alpha_rarefaction_55_4.biom   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_55_5.biom -o arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_55_5.biom -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_55_5.biom arare_max100//alpha_div//alpha_rarefaction_55_5.biom   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_55_6.biom -o arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_55_6.biom -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_55_6.biom arare_max100//alpha_div//alpha_rarefaction_55_6.biom   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_55_7.biom -o arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_55_7.biom -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_55_7.biom arare_max100//alpha_div//alpha_rarefaction_55_7.biom   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_55_8.biom -o arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_55_8.biom -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_55_8.biom arare_max100//alpha_div//alpha_rarefaction_55_8.biom   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_55_9.biom -o arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_55_9.biom -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_55_9.biom arare_max100//alpha_div//alpha_rarefaction_55_9.biom   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_64_0.biom -o arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_64_0.biom -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_64_0.biom arare_max100//alpha_div//alpha_rarefaction_64_0.biom   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_64_1.biom -o arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_64_1.biom -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_64_1.biom arare_max100//alpha_div//alpha_rarefaction_64_1.biom   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_64_2.biom -o arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_64_2.biom -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_64_2.biom arare_max100//alpha_div//alpha_rarefaction_64_2.biom   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_64_3.biom -o arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_64_3.biom -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_64_3.biom arare_max100//alpha_div//alpha_rarefaction_64_3.biom   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_64_4.biom -o arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_64_4.biom -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_64_4.biom arare_max100//alpha_div//alpha_rarefaction_64_4.biom   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_64_5.biom -o arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_64_5.biom -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_64_5.biom arare_max100//alpha_div//alpha_rarefaction_64_5.biom   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_64_6.biom -o arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_64_6.biom -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_64_6.biom arare_max100//alpha_div//alpha_rarefaction_64_6.biom   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_64_7.biom -o arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_64_7.biom -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_64_7.biom arare_max100//alpha_div//alpha_rarefaction_64_7.biom   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_64_8.biom -o arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_64_8.biom -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_64_8.biom arare_max100//alpha_div//alpha_rarefaction_64_8.biom   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_64_9.biom -o arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_64_9.biom -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_64_9.biom arare_max100//alpha_div//alpha_rarefaction_64_9.biom   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_73_0.biom -o arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_73_0.biom -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_73_0.biom arare_max100//alpha_div//alpha_rarefaction_73_0.biom   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_73_1.biom -o arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_73_1.biom -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_73_1.biom arare_max100//alpha_div//alpha_rarefaction_73_1.biom   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_73_2.biom -o arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_73_2.biom -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_73_2.biom arare_max100//alpha_div//alpha_rarefaction_73_2.biom   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_73_3.biom -o arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_73_3.biom -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_73_3.biom arare_max100//alpha_div//alpha_rarefaction_73_3.biom   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_73_4.biom -o arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_73_4.biom -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_73_4.biom arare_max100//alpha_div//alpha_rarefaction_73_4.biom   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_73_5.biom -o arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_73_5.biom -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_73_5.biom arare_max100//alpha_div//alpha_rarefaction_73_5.biom   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_73_6.biom -o arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_73_6.biom -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_73_6.biom arare_max100//alpha_div//alpha_rarefaction_73_6.biom   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_73_7.biom -o arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_73_7.biom -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_73_7.biom arare_max100//alpha_div//alpha_rarefaction_73_7.biom   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_73_8.biom -o arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_73_8.biom -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_73_8.biom arare_max100//alpha_div//alpha_rarefaction_73_8.biom   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_73_9.biom -o arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_73_9.biom -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_73_9.biom arare_max100//alpha_div//alpha_rarefaction_73_9.biom   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_82_0.biom -o arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_82_0.biom -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_82_0.biom arare_max100//alpha_div//alpha_rarefaction_82_0.biom   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_82_1.biom -o arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_82_1.biom -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_82_1.biom arare_max100//alpha_div//alpha_rarefaction_82_1.biom   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_82_2.biom -o arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_82_2.biom -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_82_2.biom arare_max100//alpha_div//alpha_rarefaction_82_2.biom   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_82_3.biom -o arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_82_3.biom -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_82_3.biom arare_max100//alpha_div//alpha_rarefaction_82_3.biom   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_82_4.biom -o arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_82_4.biom -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_82_4.biom arare_max100//alpha_div//alpha_rarefaction_82_4.biom   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_82_5.biom -o arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_82_5.biom -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_82_5.biom arare_max100//alpha_div//alpha_rarefaction_82_5.biom   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_82_6.biom -o arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_82_6.biom -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_82_6.biom arare_max100//alpha_div//alpha_rarefaction_82_6.biom   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_82_7.biom -o arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_82_7.biom -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_82_7.biom arare_max100//alpha_div//alpha_rarefaction_82_7.biom   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_82_8.biom -o arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_82_8.biom -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_82_8.biom arare_max100//alpha_div//alpha_rarefaction_82_8.biom   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_82_9.biom -o arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_82_9.biom -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_82_9.biom arare_max100//alpha_div//alpha_rarefaction_82_9.biom   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_91_0.biom -o arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_91_0.biom -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_91_0.biom arare_max100//alpha_div//alpha_rarefaction_91_0.biom   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_91_1.biom -o arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_91_1.biom -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_91_1.biom arare_max100//alpha_div//alpha_rarefaction_91_1.biom   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_91_2.biom -o arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_91_2.biom -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_91_2.biom arare_max100//alpha_div//alpha_rarefaction_91_2.biom   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_91_3.biom -o arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_91_3.biom -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_91_3.biom arare_max100//alpha_div//alpha_rarefaction_91_3.biom   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_91_4.biom -o arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_91_4.biom -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_91_4.biom arare_max100//alpha_div//alpha_rarefaction_91_4.biom   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_91_5.biom -o arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_91_5.biom -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_91_5.biom arare_max100//alpha_div//alpha_rarefaction_91_5.biom   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_91_6.biom -o arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_91_6.biom -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_91_6.biom arare_max100//alpha_div//alpha_rarefaction_91_6.biom   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_91_7.biom -o arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_91_7.biom -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_91_7.biom arare_max100//alpha_div//alpha_rarefaction_91_7.biom   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_91_8.biom -o arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_91_8.biom -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_91_8.biom arare_max100//alpha_div//alpha_rarefaction_91_8.biom   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_91_9.biom -o arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_91_9.biom -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_IB0_/alpha_rarefaction_91_9.biom arare_max100//alpha_div//alpha_rarefaction_91_9.biom   