├── README.md ├── bin ├── get_OTUabundance.sh ├── hmmer-3.0_Xander_patch.txt ├── prepare_gene_ref.sh ├── qsub_run_xander_skel.sh ├── qsub_xander_setenv.sh ├── run_xander_build.sh ├── run_xander_findStarts.sh ├── run_xander_search.sh ├── run_xander_skel.sh └── xander_setenv.sh ├── gene_resource ├── amoA_AOA │ ├── for_enone.hmm │ ├── originaldata │ │ ├── amoA_AOA.aln │ │ ├── amoA_AOA.hmm │ │ ├── amoA_AOA.seeds │ │ ├── framebot.fa │ │ └── nucl.fa │ ├── ref_aligned.faa │ └── rev_enone.hmm ├── amoA_AOB │ ├── for_enone.hmm │ ├── originaldata │ │ ├── amoA_AOB.aln │ │ ├── amoA_AOB.hmm │ │ ├── amoA_AOB.seeds │ │ ├── framebot.fa │ │ └── nucl.fa │ ├── ref_aligned.faa │ └── rev_enone.hmm ├── nifH │ ├── for_enone.hmm │ ├── originaldata │ │ ├── framebot.fa │ │ ├── nifH.hmm │ │ ├── nifH.seeds │ │ └── nucl.fa │ ├── ref_aligned.faa │ └── rev_enone.hmm ├── nirK │ ├── for_enone.hmm │ ├── originaldata │ │ ├── framebot.fa │ │ ├── nirK.hmm │ │ ├── nirK.seeds │ │ └── nucl.fa │ ├── ref_aligned.faa │ └── rev_enone.hmm ├── nirS │ ├── for_enone.hmm │ ├── originaldata │ │ ├── framebot.fa │ │ ├── nirS.hmm │ │ ├── nirS.seeds │ │ └── nucl.fa │ ├── ref_aligned.faa │ └── rev_enone.hmm ├── norB_cNor │ ├── for_enone.hmm │ ├── originaldata │ │ ├── framebot.fa │ │ ├── norB_cNor.hmm │ │ ├── norB_cNor.seeds │ │ └── nucl.fa │ ├── ref_aligned.faa │ └── rev_enone.hmm ├── norB_qNor │ ├── for_enone.hmm │ ├── originaldata │ │ ├── framebot.fa │ │ ├── norB_qNor.aln │ │ ├── norB_qNor.hmm │ │ ├── norB_qNor.seeds │ │ └── nucl.fa │ ├── ref_aligned.faa │ └── rev_enone.hmm ├── nosZ │ ├── for_enone.hmm │ ├── originaldata │ │ ├── framebot.fa │ │ ├── nosZ.aln │ │ ├── nosZ.hmm │ │ ├── nosZ.seeds │ │ └── nucl.fa │ ├── ref_aligned.faa │ └── rev_enone.hmm ├── nosZ_a2 │ ├── for_enone.hmm │ ├── originaldata │ │ ├── framebot.fa │ │ ├── nosZ_a2.aln │ │ ├── nosZ_a2.hmm │ │ ├── nosZ_a2.seeds │ │ └── nucl.fa │ ├── ref_aligned.faa │ └── rev_enone.hmm └── rplB │ ├── for_enone.hmm │ ├── originaldata │ ├── framebot.fa │ ├── 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