   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_100_0.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_100_0.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_100_0.txt arare_max100//alpha_div//alpha_rarefaction_100_0.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_100_1.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_100_1.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_100_1.txt arare_max100//alpha_div//alpha_rarefaction_100_1.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_100_2.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_100_2.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_100_2.txt arare_max100//alpha_div//alpha_rarefaction_100_2.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_100_3.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_100_3.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_100_3.txt arare_max100//alpha_div//alpha_rarefaction_100_3.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_100_4.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_100_4.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_100_4.txt arare_max100//alpha_div//alpha_rarefaction_100_4.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_100_5.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_100_5.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_100_5.txt arare_max100//alpha_div//alpha_rarefaction_100_5.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_100_6.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_100_6.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_100_6.txt arare_max100//alpha_div//alpha_rarefaction_100_6.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_100_7.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_100_7.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_100_7.txt arare_max100//alpha_div//alpha_rarefaction_100_7.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_100_8.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_100_8.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_100_8.txt arare_max100//alpha_div//alpha_rarefaction_100_8.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_100_9.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_100_9.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_100_9.txt arare_max100//alpha_div//alpha_rarefaction_100_9.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_10_0.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_10_0.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_10_0.txt arare_max100//alpha_div//alpha_rarefaction_10_0.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_10_1.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_10_1.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_10_1.txt arare_max100//alpha_div//alpha_rarefaction_10_1.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_10_2.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_10_2.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_10_2.txt arare_max100//alpha_div//alpha_rarefaction_10_2.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_10_3.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_10_3.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_10_3.txt arare_max100//alpha_div//alpha_rarefaction_10_3.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_10_4.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_10_4.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_10_4.txt arare_max100//alpha_div//alpha_rarefaction_10_4.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_10_5.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_10_5.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_10_5.txt arare_max100//alpha_div//alpha_rarefaction_10_5.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_10_6.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_10_6.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_10_6.txt arare_max100//alpha_div//alpha_rarefaction_10_6.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_10_7.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_10_7.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_10_7.txt arare_max100//alpha_div//alpha_rarefaction_10_7.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_10_8.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_10_8.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_10_8.txt arare_max100//alpha_div//alpha_rarefaction_10_8.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_10_9.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_10_9.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_10_9.txt arare_max100//alpha_div//alpha_rarefaction_10_9.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_19_0.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_19_0.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_19_0.txt arare_max100//alpha_div//alpha_rarefaction_19_0.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_19_1.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_19_1.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_19_1.txt arare_max100//alpha_div//alpha_rarefaction_19_1.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_19_2.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_19_2.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_19_2.txt arare_max100//alpha_div//alpha_rarefaction_19_2.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_19_3.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_19_3.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_19_3.txt arare_max100//alpha_div//alpha_rarefaction_19_3.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_19_4.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_19_4.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_19_4.txt arare_max100//alpha_div//alpha_rarefaction_19_4.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_19_5.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_19_5.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_19_5.txt arare_max100//alpha_div//alpha_rarefaction_19_5.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_19_6.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_19_6.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_19_6.txt arare_max100//alpha_div//alpha_rarefaction_19_6.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_19_7.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_19_7.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_19_7.txt arare_max100//alpha_div//alpha_rarefaction_19_7.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_19_8.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_19_8.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_19_8.txt arare_max100//alpha_div//alpha_rarefaction_19_8.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_19_9.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_19_9.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_19_9.txt arare_max100//alpha_div//alpha_rarefaction_19_9.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_28_0.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_28_0.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_28_0.txt arare_max100//alpha_div//alpha_rarefaction_28_0.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_28_1.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_28_1.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_28_1.txt arare_max100//alpha_div//alpha_rarefaction_28_1.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_28_2.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_28_2.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_28_2.txt arare_max100//alpha_div//alpha_rarefaction_28_2.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_28_3.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_28_3.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_28_3.txt arare_max100//alpha_div//alpha_rarefaction_28_3.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_28_4.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_28_4.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_28_4.txt arare_max100//alpha_div//alpha_rarefaction_28_4.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_28_5.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_28_5.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_28_5.txt arare_max100//alpha_div//alpha_rarefaction_28_5.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_28_6.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_28_6.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_28_6.txt arare_max100//alpha_div//alpha_rarefaction_28_6.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_28_7.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_28_7.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_28_7.txt arare_max100//alpha_div//alpha_rarefaction_28_7.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_28_8.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_28_8.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_28_8.txt arare_max100//alpha_div//alpha_rarefaction_28_8.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_28_9.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_28_9.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_28_9.txt arare_max100//alpha_div//alpha_rarefaction_28_9.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_37_0.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_37_0.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_37_0.txt arare_max100//alpha_div//alpha_rarefaction_37_0.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_37_1.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_37_1.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_37_1.txt arare_max100//alpha_div//alpha_rarefaction_37_1.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_37_2.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_37_2.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_37_2.txt arare_max100//alpha_div//alpha_rarefaction_37_2.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_37_3.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_37_3.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_37_3.txt arare_max100//alpha_div//alpha_rarefaction_37_3.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_37_4.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_37_4.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_37_4.txt arare_max100//alpha_div//alpha_rarefaction_37_4.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_37_5.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_37_5.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_37_5.txt arare_max100//alpha_div//alpha_rarefaction_37_5.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_37_6.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_37_6.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_37_6.txt arare_max100//alpha_div//alpha_rarefaction_37_6.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_37_7.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_37_7.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_37_7.txt arare_max100//alpha_div//alpha_rarefaction_37_7.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_37_8.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_37_8.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_37_8.txt arare_max100//alpha_div//alpha_rarefaction_37_8.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_37_9.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_37_9.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_37_9.txt arare_max100//alpha_div//alpha_rarefaction_37_9.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_46_0.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_46_0.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_46_0.txt arare_max100//alpha_div//alpha_rarefaction_46_0.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_46_1.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_46_1.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_46_1.txt arare_max100//alpha_div//alpha_rarefaction_46_1.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_46_2.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_46_2.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_46_2.txt arare_max100//alpha_div//alpha_rarefaction_46_2.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_46_3.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_46_3.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_46_3.txt arare_max100//alpha_div//alpha_rarefaction_46_3.txt   
   python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i arare_max100//rarefaction/rarefaction_46_4.txt -o arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_46_4.txt -t rep_set.tre -m PD_whole_tree,chao1,observed_species 
 mv arare_max100//alpha_div//ALDIV_l4D_/alpha_rarefaction_46_4.txt arare_max100//alpha_div//alpha_rarefaction_46_4.txt   