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data/s5f/HS5F_Mutability.csv
data/s5f/HS5F_Substitution.csv
data/selection-metrics/ab-choice.yaml
data/selection-metrics/slice-bins.yaml
data/selection-metrics/dtr-models/among-families-affinity-dtr-model.pickle
data/selection-metrics/dtr-models/among-families-affinity-dtr-model.pmml
data/selection-metrics/dtr-models/among-families-delta-affinity-dtr-model.pickle
data/selection-metrics/dtr-models/among-families-delta-affinity-dtr-model.pmml
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data/selection-metrics/dtr-models/within-families-affinity-dtr-model.pmml
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data/selection-metrics/dtr-models/within-families-delta-affinity-dtr-model.pmml
data/substitution-profiles/GSSPs_for_VH_genes_with_at_least_300_lineages.txt
data/substitution-profiles/GSSPs_for_VK_genes_with_at_least_300_lineages.txt
data/substitution-profiles/GSSPs_for_VL_genes_with_at_least_300_lineages.txt
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docs/parallel.md
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test/new-results/test/parameters/data/sw/seq_content.csv
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test/new-results/test/parameters/data/sw/v_gene-probs.csv
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test/new-results/test/parameters/data/sw/v_gene-v_5p_del-probs.csv
test/new-results/test/parameters/data/sw/vd_insertion_content.csv
test/new-results/test/parameters/data/sw/germline-sets/igh/extras.csv
test/new-results/test/parameters/data/sw/germline-sets/igh/ighd.fasta
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test/new-results/test/parameters/data/sw/mute-freqs/IGHV5-51_star_01.csv
test/new-results/test/parameters/simu/sw-cache.yaml
test/new-results/test/parameters/simu/hmm/all-mean-mute-freqs.csv
test/new-results/test/parameters/simu/hmm/all-mean-n-muted.csv
test/new-results/test/parameters/simu/hmm/all-probs.csv
test/new-results/test/parameters/simu/hmm/cluster_size.csv
test/new-results/test/parameters/simu/hmm/d-mean-mute-freqs.csv
test/new-results/test/parameters/simu/hmm/d-mean-n-muted.csv
test/new-results/test/parameters/simu/hmm/d_gene-d_3p_del-probs.csv
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test/new-results/test/parameters/simu/hmm/d_gene-probs.csv
test/new-results/test/parameters/simu/hmm/d_gene-vd_insertion-probs.csv
test/new-results/test/parameters/simu/hmm/dj_insertion_content.csv
test/new-results/test/parameters/simu/hmm/fv_insertion-probs.csv
test/new-results/test/parameters/simu/hmm/j-mean-mute-freqs.csv
test/new-results/test/parameters/simu/hmm/j-mean-n-muted.csv
test/new-results/test/parameters/simu/hmm/j_gene-dj_insertion-probs.csv
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test/new-results/test/parameters/simu/hmm/j_gene-probs.csv
test/new-results/test/parameters/simu/hmm/jf_insertion-probs.csv
test/new-results/test/parameters/simu/hmm/seq_content.csv
test/new-results/test/parameters/simu/hmm/v-mean-mute-freqs.csv
test/new-results/test/parameters/simu/hmm/v-mean-n-muted.csv
test/new-results/test/parameters/simu/hmm/v_gene-probs.csv
test/new-results/test/parameters/simu/hmm/v_gene-v_3p_del-probs.csv
test/new-results/test/parameters/simu/hmm/v_gene-v_5p_del-probs.csv
test/new-results/test/parameters/simu/hmm/vd_insertion_content.csv
test/new-results/test/parameters/simu/hmm/germline-sets/igh/extras.csv
test/new-results/test/parameters/simu/hmm/germline-sets/igh/ighd.fasta
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test/new-results/test/parameters/simu/hmm/hmms/IGHD1-20_star_01.yaml
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test/new-results/test/parameters/simu/sw/all-mean-mute-freqs.csv
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test/new-results/test/parameters/simu/sw/all-probs.csv
test/new-results/test/parameters/simu/sw/cluster_size.csv
test/new-results/test/parameters/simu/sw/d-mean-mute-freqs.csv
test/new-results/test/parameters/simu/sw/d-mean-n-muted.csv
test/new-results/test/parameters/simu/sw/d_gene-d_3p_del-probs.csv
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test/new-results/test/parameters/simu/sw/dj_insertion_content.csv
test/new-results/test/parameters/simu/sw/fv_insertion-probs.csv
test/new-results/test/parameters/simu/sw/j-mean-mute-freqs.csv
test/new-results/test/parameters/simu/sw/j-mean-n-muted.csv
test/new-results/test/parameters/simu/sw/j_gene-dj_insertion-probs.csv
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test/new-results/test/parameters/simu/sw/j_gene-probs.csv
test/new-results/test/parameters/simu/sw/jf_insertion-probs.csv
test/new-results/test/parameters/simu/sw/seq_content.csv
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test/new-results/test/parameters/simu/sw/v_gene-v_3p_del-probs.csv
test/new-results/test/parameters/simu/sw/v_gene-v_5p_del-probs.csv
test/new-results/test/parameters/simu/sw/vd_insertion_content.csv
test/new-results/test/parameters/simu/sw/germline-sets/igh/extras.csv
test/new-results/test/parameters/simu/sw/germline-sets/igh/ighd.fasta
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test/paired/new-results/test/parameters/simu/igh/hmm/hmms/IGHJ3_star_02.yaml
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test/paired/new-results/test/parameters/simu/igh/sw/v-mean-mute-freqs.csv
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test/paired/new-results/test/parameters/simu/igh/sw/vd_insertion_content.csv
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test/paired/new-results/test/parameters/simu/igh/sw/hmms/IGHV1-69_star_04.yaml
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test/paired/new-results/test/parameters/simu/igh/sw/hmms/IGHV3-7_star_01.yaml
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test/paired/ref-results/seed-partition-new-simu/seeds/3542bd38d8-igh+3542bd38d8-igk/igh+igk/partition-igh.yaml
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test/paired/ref-results/seed-partition-new-simu/seeds/3542bd38d8-igh+3542bd38d8-igk/single-chain/partition-igh.yaml
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test/paired/ref-results/seed-partition-new-simu/seeds/3542bd38d8-igh+3542bd38d8-igk/single-chain/partition-igl.yaml
test/paired/ref-results/subset-partition-new-simu/merged-partition.log
test/paired/ref-results/subset-partition-new-simu/partition-igh.yaml
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test/paired/ref-results/subset-partition-new-simu/igh+igk/partition-igh.yaml
test/paired/ref-results/subset-partition-new-simu/igh+igk/partition-igk.yaml
test/paired/ref-results/subset-partition-new-simu/igh+igl/partition-igh.yaml
test/paired/ref-results/subset-partition-new-simu/igh+igl/partition-igl.yaml
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test/paired/ref-results/subset-partition-new-simu/isub-0/meta.yaml
test/paired/ref-results/subset-partition-new-simu/isub-0/partition-igh.yaml
test/paired/ref-results/subset-partition-new-simu/isub-0/partition-igk.yaml
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test/paired/ref-results/subset-partition-new-simu/isub-0/igh+igk/partition-igh.yaml
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test/paired/ref-results/subset-partition-new-simu/isub-0/igh+igl/partition-igh.yaml
test/paired/ref-results/subset-partition-new-simu/isub-0/igh+igl/partition-igl.yaml
test/paired/ref-results/subset-partition-new-simu/isub-0/parameters/igh/sw-cache.yaml
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test/ref-results/test/parameters/simu/true/germline-sets/igh/ighv.fasta
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