diff --git a/FROGS b/FROGS
new file mode 100644
index 0000000000000000000000000000000000000000..7f3bdfe0fbae7a8292d2e1c307497d8e25b7b58c
--- /dev/null
+++ b/FROGS
@@ -0,0 +1,15 @@
+###FROGS for 16S
+### CHECK PARAMETERS 
+conda activate frogs-3.2.2
+preprocess.py illumina --input-archive ffiles.tar.gz --min-amplicon-size 200 --max-amplicon-size 700 --merge-software flash --five-prim-primer CCTACGGGAGGCAGCAG --three-prim-primer ATTAGAWACCCVHGTAGTCC --R1-size 300 --R2-size 300 --nb-cpus 8 --output-dereplicated FROGS/preprocess2.fasta --output-count FROGS/preprocess2.tsv --summary FROGS/preprocess2.html --log-file FROGS/preprocess2.log
+
+clustering.py --input-fasta FROGS/preprocess.fasta --input-count FROGS/preprocess.tsv --distance 1 --fastidious --nb-cpus 8 --log-file FROGS/clustering.log --output-biom FROGS/clustering.biom --output-fasta FROGS/clustering.fasta --output-compo FROGS/clustering_otu_compositions.tsv
+
+remove_chimera.py --input-fasta FROGS/clustering.fasta --input-biom FROGS/clustering.biom --non-chimera FROGS/remove_chimera.fasta --nb-cpus 8 --log-file FROGS/remove_chimera.log --out-abundance FROGS/remove_chimera.biom --summary FROGS/remove_chimera.html
+
+otu_filters.py --input-fasta FROGS/remove_chimera.fasta --input-biom FROGS/remove_chimera.biom --output-fasta FROGS/filters.fasta --nb-cpus 8 --log-file FROGS/filters.log --output-biom FROGS/filters.biom --summary FROGS/filters.html --excluded FROGS/filters_excluded.tsv --contaminant /db/frogs_databanks/contaminants/phi.fa --min-sample-presence 1 --min-abundance 0.00005
+
+affiliation_OTU.py --input-fasta FROGS/filters.fasta --input-biom FROGS/filters.biom --nb-cpus 8 --log-file FROGS/affiliation.log --output-biom FROGS/affiliation.biom --summary FROGS/affiliation.html --reference /db/frogs_databanks/assignation/silva_138_16S/silva_138_16S.fasta
+
+biom_to_tsv.py --input-biom FROGS/affiliation.biom --input-fasta FROGS/filters.fasta --output-tsv FROGS/affiliation.tsv --output-multi-affi FROGS/multi_aff.tsv --log-file FROGS/biom_to_tsv.log  
+conda deactivate
diff --git a/HMM_Carbonic_anhydrases b/HMM_Carbonic_anhydrases
new file mode 100644
index 0000000000000000000000000000000000000000..180cb9ab8c8970a6aa48b6a62b795d25e6e6a3f3
--- /dev/null
+++ b/HMM_Carbonic_anhydrases
@@ -0,0 +1,87 @@
+# HMM
+mkdir hmmXXb2/
+cd hmmXXb2/
+hmmsearch --tblout cluster3010.out -E 1.70E-58 /projet/genosol/work/SOLCA/script/CA_HMM/HMM/HMM/cluster3010.faa.subset.faa.hmm ../fragXXb2/fraggenscanXXb2.faa
+hmmsearch --tblout cluster3011.out -E 3.40E-10 /projet/genosol/work/SOLCA/script/CA_HMM/HMM/HMM/cluster3011.faa.subset.faa.hmm ../fragXXb2/fraggenscanXXb2.faa  
+hmmsearch --tblout cluster30113.out -E 1.50E-53 /projet/genosol/work/SOLCA/script/CA_HMM/HMM/HMM/cluster30113.faa.subset.faa.hmm ../fragXXb2/fraggenscanXXb2.faa  
+hmmsearch --tblout cluster30117.out -E 1.40E-48 /projet/genosol/work/SOLCA/script/CA_HMM/HMM/HMM/cluster30117.faa.subset.faa.hmm ../fragXXb2/fraggenscanXXb2.faa  
+hmmsearch --tblout cluster3012.out -E 7.00E-81 /projet/genosol/work/SOLCA/script/CA_HMM/HMM/HMM/cluster3012.faa.subset.faa.hmm ../fragXXb2/fraggenscanXXb2.faa  
+hmmsearch --tblout cluster30120.out -E 1.50E-57 /projet/genosol/work/SOLCA/script/CA_HMM/HMM/HMM/cluster30120.faa.subset.faa.hmm ../fragXXb2/fraggenscanXXb2.faa  
+hmmsearch --tblout cluster30121.out -E 6.30E-57 /projet/genosol/work/SOLCA/script/CA_HMM/HMM/HMM/cluster30121.faa.subset.faa.hmm ../fragXXb2/fraggenscanXXb2.faa  
+hmmsearch --tblout cluster301242.out -E 1.20E-140 /projet/genosol/work/SOLCA/script/CA_HMM/HMM/HMM/cluster301242.faa.subset.faa.hmm ../fragXXb2/fraggenscanXXb2.faa  
+hmmsearch --tblout cluster30129.out -E 2.90E-05 /projet/genosol/work/SOLCA/script/CA_HMM/HMM/HMM/cluster30129.faa.subset.faa.hmm ../fragXXb2/fraggenscanXXb2.faa  
+hmmsearch --tblout cluster3013.out -E 2.90E-59 /projet/genosol/work/SOLCA/script/CA_HMM/HMM/HMM/cluster3013.faa.subset.faa.hmm ../fragXXb2/fraggenscanXXb2.faa  
+hmmsearch --tblout cluster30130.out -E 6.50E-84 /projet/genosol/work/SOLCA/script/CA_HMM/HMM/HMM/cluster30130.faa.subset.faa.hmm ../fragXXb2/fraggenscanXXb2.faa  
+hmmsearch --tblout cluster30139.out -E 8.70E-81 /projet/genosol/work/SOLCA/script/CA_HMM/HMM/HMM/cluster30139.faa.subset.faa.hmm ../fragXXb2/fraggenscanXXb2.faa  
+hmmsearch --tblout cluster3014.out -E 6.80E-76 /projet/genosol/work/SOLCA/script/CA_HMM/HMM/HMM/cluster3014.faa.subset.faa.hmm ../fragXXb2/fraggenscanXXb2.faa  
+hmmsearch --tblout cluster30140.out -E 8.20E-88 /projet/genosol/work/SOLCA/script/CA_HMM/HMM/HMM/cluster30140.faa.subset.faa.hmm ../fragXXb2/fraggenscanXXb2.faa  
+hmmsearch --tblout cluster30144.out -E 5.30E-64 /projet/genosol/work/SOLCA/script/CA_HMM/HMM/HMM/cluster30144.faa.subset.faa.hmm ../fragXXb2/fraggenscanXXb2.faa  
+hmmsearch --tblout cluster30145.out -E 1.40E-36 /projet/genosol/work/SOLCA/script/CA_HMM/HMM/HMM/cluster30145.faa.subset.faa.hmm ../fragXXb2/fraggenscanXXb2.faa  
+hmmsearch --tblout cluster30147.out -E 1.70E-116 /projet/genosol/work/SOLCA/script/CA_HMM/HMM/HMM/cluster30147.faa.subset.faa.hmm ../fragXXb2/fraggenscanXXb2.faa  
+hmmsearch --tblout cluster30149.out -E 3.70E-28 /projet/genosol/work/SOLCA/script/CA_HMM/HMM/HMM/cluster30149.faa.subset.faa.hmm ../fragXXb2/fraggenscanXXb2.faa  
+hmmsearch --tblout cluster3015.out -E 1.40E-53 /projet/genosol/work/SOLCA/script/CA_HMM/HMM/HMM/cluster3015.faa.subset.faa.hmm ../fragXXb2/fraggenscanXXb2.faa  
+hmmsearch --tblout cluster30150.out -E 4.70E-52 /projet/genosol/work/SOLCA/script/CA_HMM/HMM/HMM/cluster30150.faa.subset.faa.hmm ../fragXXb2/fraggenscanXXb2.faa  
+hmmsearch --tblout cluster30154.out -E 4.80E-35 /projet/genosol/work/SOLCA/script/CA_HMM/HMM/HMM/cluster30154.faa.subset.faa.hmm ../fragXXb2/fraggenscanXXb2.faa  
+hmmsearch --tblout cluster30155.out -E 3.80E-70 /projet/genosol/work/SOLCA/script/CA_HMM/HMM/HMM/cluster30155.faa.subset.faa.hmm ../fragXXb2/fraggenscanXXb2.faa  
+hmmsearch --tblout cluster30157.out -E 3.50E-170 /projet/genosol/work/SOLCA/script/CA_HMM/HMM/HMM/cluster30157.faa.subset.faa.hmm ../fragXXb2/fraggenscanXXb2.faa  
+hmmsearch --tblout cluster30158.out -E 2.20E-77 /projet/genosol/work/SOLCA/script/CA_HMM/HMM/HMM/cluster30158.faa.subset.faa.hmm ../fragXXb2/fraggenscanXXb2.faa  
+hmmsearch --tblout cluster30160.out -E 5.00E-30 /projet/genosol/work/SOLCA/script/CA_HMM/HMM/HMM/cluster30160.faa.subset.faa.hmm ../fragXXb2/fraggenscanXXb2.faa  
+hmmsearch --tblout cluster30161.out -E 1.70E-71 /projet/genosol/work/SOLCA/script/CA_HMM/HMM/HMM/cluster30161.faa.subset.faa.hmm ../fragXXb2/fraggenscanXXb2.faa  
+hmmsearch --tblout cluster30162.out -E 3.50E-51 /projet/genosol/work/SOLCA/script/CA_HMM/HMM/HMM/cluster30162.faa.subset.faa.hmm ../fragXXb2/fraggenscanXXb2.faa  
+hmmsearch --tblout cluster30163.out -E 1.50E-106 /projet/genosol/work/SOLCA/script/CA_HMM/HMM/HMM/cluster30163.faa.subset.faa.hmm ../fragXXb2/fraggenscanXXb2.faa  
+hmmsearch --tblout cluster30168.out -E 5.50E-47 /projet/genosol/work/SOLCA/script/CA_HMM/HMM/HMM/cluster30168.faa.subset.faa.hmm ../fragXXb2/fraggenscanXXb2.faa  
+hmmsearch --tblout cluster30171.out -E 3.80E-76 /projet/genosol/work/SOLCA/script/CA_HMM/HMM/HMM/cluster30171.faa.subset.faa.hmm ../fragXXb2/fraggenscanXXb2.faa  
+hmmsearch --tblout cluster30173.out -E 2.10E-110 /projet/genosol/work/SOLCA/script/CA_HMM/HMM/HMM/cluster30173.faa.subset.faa.hmm ../fragXXb2/fraggenscanXXb2.faa  
+hmmsearch --tblout cluster30175.out -E 1.60E-106 /projet/genosol/work/SOLCA/script/CA_HMM/HMM/HMM/cluster30175.faa.subset.faa.hmm ../fragXXb2/fraggenscanXXb2.faa  
+hmmsearch --tblout cluster30176.out -E 2.70E-62 /projet/genosol/work/SOLCA/script/CA_HMM/HMM/HMM/cluster30176.faa.subset.faa.hmm ../fragXXb2/fraggenscanXXb2.faa  
+hmmsearch --tblout cluster30177.out -E 4.40E-22 /projet/genosol/work/SOLCA/script/CA_HMM/HMM/HMM/cluster30177.faa.subset.faa.hmm ../fragXXb2/fraggenscanXXb2.faa  
+hmmsearch --tblout cluster30184.out -E 2.30E-55 /projet/genosol/work/SOLCA/script/CA_HMM/HMM/HMM/cluster30184.faa.subset.faa.hmm ../fragXXb2/fraggenscanXXb2.faa  
+hmmsearch --tblout cluster30191.out -E 1.90E-77 /projet/genosol/work/SOLCA/script/CA_HMM/HMM/HMM/cluster30191.faa.subset.faa.hmm ../fragXXb2/fraggenscanXXb2.faa  
+hmmsearch --tblout cluster30202.out -E 3.30E-82 /projet/genosol/work/SOLCA/script/CA_HMM/HMM/HMM/cluster30202.faa.subset.faa.hmm ../fragXXb2/fraggenscanXXb2.faa  
+hmmsearch --tblout cluster30207.out -E 6.60E-35 /projet/genosol/work/SOLCA/script/CA_HMM/HMM/HMM/cluster30207.faa.subset.faa.hmm ../fragXXb2/fraggenscanXXb2.faa  
+hmmsearch --tblout cluster30208.out -E 2.10E-48 /projet/genosol/work/SOLCA/script/CA_HMM/HMM/HMM/cluster30208.faa.subset.faa.hmm ../fragXXb2/fraggenscanXXb2.faa  
+hmmsearch --tblout cluster30209.out -E 2.40E-54 /projet/genosol/work/SOLCA/script/CA_HMM/HMM/HMM/cluster30209.faa.subset.faa.hmm ../fragXXb2/fraggenscanXXb2.faa  
+hmmsearch --tblout cluster30212.out -E 3.30E-91 /projet/genosol/work/SOLCA/script/CA_HMM/HMM/HMM/cluster30212.faa.subset.faa.hmm ../fragXXb2/fraggenscanXXb2.faa  
+hmmsearch --tblout cluster30214.out -E 5.00E-92 /projet/genosol/work/SOLCA/script/CA_HMM/HMM/HMM/cluster30214.faa.subset.faa.hmm ../fragXXb2/fraggenscanXXb2.faa  
+hmmsearch --tblout cluster30221.out -E 7.70E-52 /projet/genosol/work/SOLCA/script/CA_HMM/HMM/HMM/cluster30221.faa.subset.faa.hmm ../fragXXb2/fraggenscanXXb2.faa  
+hmmsearch --tblout cluster30225.out -E 2.50E-90 /projet/genosol/work/SOLCA/script/CA_HMM/HMM/HMM/cluster30225.faa.subset.faa.hmm ../fragXXb2/fraggenscanXXb2.faa  
+hmmsearch --tblout cluster30230.out -E 4.90E-57 /projet/genosol/work/SOLCA/script/CA_HMM/HMM/HMM/cluster30230.faa.subset.faa.hmm ../fragXXb2/fraggenscanXXb2.faa  
+hmmsearch --tblout cluster30232.out -E 2.10E-56 /projet/genosol/work/SOLCA/script/CA_HMM/HMM/HMM/cluster30232.faa.subset.faa.hmm ../fragXXb2/fraggenscanXXb2.faa  
+hmmsearch --tblout cluster30238.out -E 9.80E-79 /projet/genosol/work/SOLCA/script/CA_HMM/HMM/HMM/cluster30238.faa.subset.faa.hmm ../fragXXb2/fraggenscanXXb2.faa  
+hmmsearch --tblout cluster30242.out -E 3.10E-54 /projet/genosol/work/SOLCA/script/CA_HMM/HMM/HMM/cluster30242.faa.subset.faa.hmm ../fragXXb2/fraggenscanXXb2.faa  
+hmmsearch --tblout cluster30250.out -E 4.40E-55 /projet/genosol/work/SOLCA/script/CA_HMM/HMM/HMM/cluster30250.faa.subset.faa.hmm ../fragXXb2/fraggenscanXXb2.faa  
+hmmsearch --tblout cluster30252.out -E 1.10E-51 /projet/genosol/work/SOLCA/script/CA_HMM/HMM/HMM/cluster30252.faa.subset.faa.hmm ../fragXXb2/fraggenscanXXb2.faa  
+hmmsearch --tblout cluster30254.out -E 1.20E-70 /projet/genosol/work/SOLCA/script/CA_HMM/HMM/HMM/cluster30254.faa.subset.faa.hmm ../fragXXb2/fraggenscanXXb2.faa  
+hmmsearch --tblout cluster30258.out -E 1.20E-57 /projet/genosol/work/SOLCA/script/CA_HMM/HMM/HMM/cluster30258.faa.subset.faa.hmm ../fragXXb2/fraggenscanXXb2.faa  
+hmmsearch --tblout cluster30264.out -E 3.10E-58 /projet/genosol/work/SOLCA/script/CA_HMM/HMM/HMM/cluster30264.faa.subset.faa.hmm ../fragXXb2/fraggenscanXXb2.faa  
+hmmsearch --tblout cluster3027.out -E 2.20E-159 /projet/genosol/work/SOLCA/script/CA_HMM/HMM/HMM/cluster3027.faa.subset.faa.hmm ../fragXXb2/fraggenscanXXb2.faa  
+hmmsearch --tblout cluster303.out -E 1.90E-119 /projet/genosol/work/SOLCA/script/CA_HMM/HMM/HMM/cluster303.faa.subset.faa.hmm ../fragXXb2/fraggenscanXXb2.faa  
+hmmsearch --tblout cluster30384.out -E 4.00E-97 /projet/genosol/work/SOLCA/script/CA_HMM/HMM/HMM/cluster30384.faa.subset.faa.hmm ../fragXXb2/fraggenscanXXb2.faa  
+hmmsearch --tblout cluster30407.out -E 2.30E-100 /projet/genosol/work/SOLCA/script/CA_HMM/HMM/HMM/cluster30407.faa.subset.faa.hmm ../fragXXb2/fraggenscanXXb2.faa  
+hmmsearch --tblout cluster30414.out -E 3.00E-103 /projet/genosol/work/SOLCA/script/CA_HMM/HMM/HMM/cluster30414.faa.subset.faa.hmm ../fragXXb2/fraggenscanXXb2.faa  
+hmmsearch --tblout cluster30425.out -E 2.80E-30 /projet/genosol/work/SOLCA/script/CA_HMM/HMM/HMM/cluster30425.faa.subset.faa.hmm ../fragXXb2/fraggenscanXXb2.faa  
+hmmsearch --tblout cluster30427.out -E 3.00E-83 /projet/genosol/work/SOLCA/script/CA_HMM/HMM/HMM/cluster30427.faa.subset.faa.hmm ../fragXXb2/fraggenscanXXb2.faa  
+hmmsearch --tblout cluster30467.out -E 1.80E-43 /projet/genosol/work/SOLCA/script/CA_HMM/HMM/HMM/cluster30467.faa.subset.faa.hmm ../fragXXb2/fraggenscanXXb2.faa  
+hmmsearch --tblout cluster30468.out -E 3.50E-70 /projet/genosol/work/SOLCA/script/CA_HMM/HMM/HMM/cluster30468.faa.subset.faa.hmm ../fragXXb2/fraggenscanXXb2.faa  
+hmmsearch --tblout cluster30561.out -E 5.10E-129 /projet/genosol/work/SOLCA/script/CA_HMM/HMM/HMM/cluster30561.faa.subset.faa.hmm ../fragXXb2/fraggenscanXXb2.faa  
+hmmsearch --tblout cluster30566.out -E 2.20E-134 /projet/genosol/work/SOLCA/script/CA_HMM/HMM/HMM/cluster30566.faa.subset.faa.hmm ../fragXXb2/fraggenscanXXb2.faa  
+hmmsearch --tblout cluster30580.out -E 1.80E-92 /projet/genosol/work/SOLCA/script/CA_HMM/HMM/HMM/cluster30580.faa.subset.faa.hmm ../fragXXb2/fraggenscanXXb2.faa  
+hmmsearch --tblout cluster306.out -E 2.40E-57 /projet/genosol/work/SOLCA/script/CA_HMM/HMM/HMM/cluster306.faa.subset.faa.hmm ../fragXXb2/fraggenscanXXb2.faa  
+hmmsearch --tblout cluster30606.out -E 2.80E-23 /projet/genosol/work/SOLCA/script/CA_HMM/HMM/HMM/cluster30606.faa.subset.faa.hmm ../fragXXb2/fraggenscanXXb2.faa  
+hmmsearch --tblout cluster30621.out -E 3.30E-42 /projet/genosol/work/SOLCA/script/CA_HMM/HMM/HMM/cluster30621.faa.subset.faa.hmm ../fragXXb2/fraggenscanXXb2.faa  
+hmmsearch --tblout cluster30627.out -E 2.20E-49 /projet/genosol/work/SOLCA/script/CA_HMM/HMM/HMM/cluster30627.faa.subset.faa.hmm ../fragXXb2/fraggenscanXXb2.faa  
+hmmsearch --tblout cluster30628.out -E 4.80E-39 /projet/genosol/work/SOLCA/script/CA_HMM/HMM/HMM/cluster30628.faa.subset.faa.hmm ../fragXXb2/fraggenscanXXb2.faa  
+hmmsearch --tblout cluster30629.out -E 9.00E-52 /projet/genosol/work/SOLCA/script/CA_HMM/HMM/HMM/cluster30629.faa.subset.faa.hmm ../fragXXb2/fraggenscanXXb2.faa  
+hmmsearch --tblout cluster307.out -E 4.60E-30 /projet/genosol/work/SOLCA/script/CA_HMM/HMM/HMM/cluster307.faa.subset.faa.hmm ../fragXXb2/fraggenscanXXb2.faa  
+hmmsearch --tblout cluster30754.out -E 5.90E-84 /projet/genosol/work/SOLCA/script/CA_HMM/HMM/HMM/cluster30754.faa.subset.faa.hmm ../fragXXb2/fraggenscanXXb2.faa  
+hmmsearch --tblout cluster3085.out -E 9.60E-112 /projet/genosol/work/SOLCA/script/CA_HMM/HMM/HMM/cluster3085.faa.subset.faa.hmm ../fragXXb2/fraggenscanXXb2.faa  
+hmmsearch --tblout cluster30879.out -E 9.20E-65 /projet/genosol/work/SOLCA/script/CA_HMM/HMM/HMM/cluster30879.faa.subset.faa.hmm ../fragXXb2/fraggenscanXXb2.faa  
+hmmsearch --tblout cluster3088.out -E 1.70E-15 /projet/genosol/work/SOLCA/script/CA_HMM/HMM/HMM/cluster3088.faa.subset.faa.hmm ../fragXXb2/fraggenscanXXb2.faa  
+hmmsearch --tblout cluster309.out -E 3.20E-60 /projet/genosol/work/SOLCA/script/CA_HMM/HMM/HMM/cluster309.faa.subset.faa.hmm ../fragXXb2/fraggenscanXXb2.faa  
+hmmsearch --tblout cluster3092.out -E 2.10E-34 /projet/genosol/work/SOLCA/script/CA_HMM/HMM/HMM/cluster3092.faa.subset.faa.hmm ../fragXXb2/fraggenscanXXb2.faa  
+hmmsearch --tblout cluster3093.out -E 2.40E-75 /projet/genosol/work/SOLCA/script/CA_HMM/HMM/HMM/cluster3093.faa.subset.faa.hmm ../fragXXb2/fraggenscanXXb2.faa  
+hmmsearch --tblout cluster3095.out -E 1.10E-62 /projet/genosol/work/SOLCA/script/CA_HMM/HMM/HMM/cluster3095.faa.subset.faa.hmm ../fragXXb2/fraggenscanXXb2.faa  
+hmmsearch --tblout cluster30957.out -E 9.70E-137 /projet/genosol/work/SOLCA/script/CA_HMM/HMM/HMM/cluster30957.faa.subset.faa.hmm ../fragXXb2/fraggenscanXXb2.faa  
+sed -n -e '/Query:/,/Domain/{ /cluster/ p;/TRINITY/ p;}' ../../monsterXXb2_o > txt  
+awk '{if($0~"cluster"){a=$2}if($8==1){print a$o}}' txt > hmmcaXXb2_out.txt  
+awk '{print $10}' hmmcaXXb2_out.txt > listeXXb2