   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_46_5.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_46_5.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_46_5.txt arare_max100//alpha_div//alpha_rarefaction_46_5.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_46_6.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_46_6.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_46_6.txt arare_max100//alpha_div//alpha_rarefaction_46_6.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_46_7.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_46_7.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_46_7.txt arare_max100//alpha_div//alpha_rarefaction_46_7.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_46_8.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_46_8.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_46_8.txt arare_max100//alpha_div//alpha_rarefaction_46_8.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_46_9.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_46_9.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_46_9.txt arare_max100//alpha_div//alpha_rarefaction_46_9.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_55_0.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_55_0.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_55_0.txt arare_max100//alpha_div//alpha_rarefaction_55_0.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_55_1.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_55_1.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_55_1.txt arare_max100//alpha_div//alpha_rarefaction_55_1.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_55_2.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_55_2.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_55_2.txt arare_max100//alpha_div//alpha_rarefaction_55_2.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_55_3.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_55_3.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_55_3.txt arare_max100//alpha_div//alpha_rarefaction_55_3.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_55_4.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_55_4.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_55_4.txt arare_max100//alpha_div//alpha_rarefaction_55_4.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_55_5.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_55_5.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_55_5.txt arare_max100//alpha_div//alpha_rarefaction_55_5.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_55_6.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_55_6.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_55_6.txt arare_max100//alpha_div//alpha_rarefaction_55_6.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_55_7.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_55_7.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_55_7.txt arare_max100//alpha_div//alpha_rarefaction_55_7.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_55_8.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_55_8.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_55_8.txt arare_max100//alpha_div//alpha_rarefaction_55_8.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_55_9.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_55_9.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_55_9.txt arare_max100//alpha_div//alpha_rarefaction_55_9.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_64_0.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_64_0.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_64_0.txt arare_max100//alpha_div//alpha_rarefaction_64_0.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_64_1.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_64_1.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_64_1.txt arare_max100//alpha_div//alpha_rarefaction_64_1.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_64_2.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_64_2.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_64_2.txt arare_max100//alpha_div//alpha_rarefaction_64_2.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_64_3.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_64_3.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_64_3.txt arare_max100//alpha_div//alpha_rarefaction_64_3.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_64_4.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_64_4.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_64_4.txt arare_max100//alpha_div//alpha_rarefaction_64_4.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_64_5.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_64_5.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_64_5.txt arare_max100//alpha_div//alpha_rarefaction_64_5.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_64_6.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_64_6.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_64_6.txt arare_max100//alpha_div//alpha_rarefaction_64_6.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_64_7.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_64_7.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_64_7.txt arare_max100//alpha_div//alpha_rarefaction_64_7.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_64_8.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_64_8.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_64_8.txt arare_max100//alpha_div//alpha_rarefaction_64_8.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_64_9.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_64_9.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_64_9.txt arare_max100//alpha_div//alpha_rarefaction_64_9.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_73_0.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_73_0.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_73_0.txt arare_max100//alpha_div//alpha_rarefaction_73_0.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_73_1.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_73_1.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_73_1.txt arare_max100//alpha_div//alpha_rarefaction_73_1.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_73_2.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_73_2.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_73_2.txt arare_max100//alpha_div//alpha_rarefaction_73_2.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_73_3.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_73_3.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_73_3.txt arare_max100//alpha_div//alpha_rarefaction_73_3.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_73_4.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_73_4.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_73_4.txt arare_max100//alpha_div//alpha_rarefaction_73_4.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_73_5.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_73_5.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_73_5.txt arare_max100//alpha_div//alpha_rarefaction_73_5.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_73_6.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_73_6.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_73_6.txt arare_max100//alpha_div//alpha_rarefaction_73_6.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_73_7.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_73_7.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_73_7.txt arare_max100//alpha_div//alpha_rarefaction_73_7.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_73_8.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_73_8.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_73_8.txt arare_max100//alpha_div//alpha_rarefaction_73_8.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_73_9.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_73_9.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_73_9.txt arare_max100//alpha_div//alpha_rarefaction_73_9.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_82_0.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_82_0.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_82_0.txt arare_max100//alpha_div//alpha_rarefaction_82_0.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_82_1.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_82_1.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_82_1.txt arare_max100//alpha_div//alpha_rarefaction_82_1.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_82_2.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_82_2.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_82_2.txt arare_max100//alpha_div//alpha_rarefaction_82_2.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_82_3.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_82_3.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_82_3.txt arare_max100//alpha_div//alpha_rarefaction_82_3.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_82_4.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_82_4.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_82_4.txt arare_max100//alpha_div//alpha_rarefaction_82_4.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_82_5.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_82_5.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_82_5.txt arare_max100//alpha_div//alpha_rarefaction_82_5.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_82_6.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_82_6.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_82_6.txt arare_max100//alpha_div//alpha_rarefaction_82_6.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_82_7.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_82_7.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_82_7.txt arare_max100//alpha_div//alpha_rarefaction_82_7.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_82_8.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_82_8.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_82_8.txt arare_max100//alpha_div//alpha_rarefaction_82_8.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_82_9.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_82_9.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_82_9.txt arare_max100//alpha_div//alpha_rarefaction_82_9.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_91_0.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_91_0.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_91_0.txt arare_max100//alpha_div//alpha_rarefaction_91_0.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_91_1.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_91_1.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_91_1.txt arare_max100//alpha_div//alpha_rarefaction_91_1.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_91_2.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_91_2.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_91_2.txt arare_max100//alpha_div//alpha_rarefaction_91_2.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_91_3.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_91_3.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_91_3.txt arare_max100//alpha_div//alpha_rarefaction_91_3.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_91_4.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_91_4.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_91_4.txt arare_max100//alpha_div//alpha_rarefaction_91_4.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_91_5.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_91_5.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_91_5.txt arare_max100//alpha_div//alpha_rarefaction_91_5.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_91_6.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_91_6.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_91_6.txt arare_max100//alpha_div//alpha_rarefaction_91_6.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_91_7.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_91_7.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_91_7.txt arare_max100//alpha_div//alpha_rarefaction_91_7.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_91_8.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_91_8.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_91_8.txt arare_max100//alpha_div//alpha_rarefaction_91_8.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_91_9.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_91_9.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_91_9.txt arare_max100//alpha_div//alpha_rarefaction_91_9.txt   