diff --git a/README.md b/README.md index 884f47a87681a6187c26667461d4a7dcf8f6e7e9..7983acc17175013318c5bfb303699227af696434 100644 --- a/README.md +++ b/README.md @@ -6,14 +6,15 @@ Bonhomme, Vaysset, Ednacot, Rodrigues, Cury, Hernandez Trejo, Benaroch, Morehous ### Directory - `dev/initial_mixed_detection` : Initial detection of SIR2 subfamily and SIRim proteins -- `dev/fam118b/1_detection` : Detection of SIRim subfamily proteins -- `dev/fam118b/2_align` : Alignment of SIRim subfamily proteins -- `dev/fam118b/3_iqtree_sirim_domain`: Phylogeny of SIRim subfamily proteins -- `dev/fam118b/3.1_additional_trees`: Phylogeny of SIRim subfamily proteins -- `dev/fam118b/3.2_phylo_full_protein`: Phylogeny of SIRim subfamily proteins -- `dev/fam118b/3.3_phylo_euk`: Phylogeny of SIRim subfamily proteins -- `dev/fam118b/4_defense_systems`: Detection of which of the SIR2 and SIRim subfamily proteins are involved in known defense systems (DefenseFinder) / are in genomic contexts enriched in defense systems +- `dev/sirim/1_detection` : Detection of SIRim subfamily proteins +- `dev/sirim/2_align` : Alignment of SIRim subfamily proteins +- `dev/sirim/3_phylo_sirim_domain`: Phylogeny of SIRim subfamily proteins +- `dev/sirim/3.1_additional_trees`: Phylogeny of SIRim subfamily proteins +- `dev/sirim/3.2_phylo_full_protein`: Phylogeny of SIRim subfamily proteins +- `dev/sirim/3.3_phylo_euk`: Phylogeny of SIRim subfamily proteins +- `dev/sirim/4_defense_systems`: Detection of which of the SIR2 and SIRim subfamily proteins are involved in known defense systems (DefenseFinder) / are in genomic contexts enriched in defense systems +- `dev/sirim/5_focus_eukaryotes` : Analyses regaring clades of eukaryotic SIRim (Figure 4, Figures S6-S8) - `dev/sirtuins/1_detection` : Detection of SIR2 subfamily proteins -- `dev/sirtuins/sir2_sir2-like` : Joint phylogeny of SIR2 and SIRim subfamily proteins +- `dev/phylo_sir2_sirim` : Joint phylogeny of SIR2 and SIRim subfamily proteins This repository is currently being updated. diff --git a/dev/sirtuins/detection/1_round/data/SIRT1_refseq_orthologs.fasta b/dev/sirtuins/1_detection/1_round/data/SIRT1_refseq_orthologs.fasta similarity index 100% rename from dev/sirtuins/detection/1_round/data/SIRT1_refseq_orthologs.fasta rename to dev/sirtuins/1_detection/1_round/data/SIRT1_refseq_orthologs.fasta diff --git a/dev/sirtuins/detection/1_round/data/SIRT2_refseq_orthologs.fasta b/dev/sirtuins/1_detection/1_round/data/SIRT2_refseq_orthologs.fasta similarity index 100% rename from dev/sirtuins/detection/1_round/data/SIRT2_refseq_orthologs.fasta rename to dev/sirtuins/1_detection/1_round/data/SIRT2_refseq_orthologs.fasta diff --git a/dev/sirtuins/detection/1_round/data/SIRT3_refseq_orthologs.fasta b/dev/sirtuins/1_detection/1_round/data/SIRT3_refseq_orthologs.fasta similarity index 100% rename from dev/sirtuins/detection/1_round/data/SIRT3_refseq_orthologs.fasta rename to dev/sirtuins/1_detection/1_round/data/SIRT3_refseq_orthologs.fasta diff 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a/dev/sirtuins/detection/2_round/results/1e-05_bs-gt-110_qcov-gt-80_len-200-1500/align/sirtuins_round-2_kingdom=euk_1e-05_bs-gt-110_qcov-gt-80_len-200-1500_50-80_rep_seq_19602-28711.fa b/dev/sirtuins/1_detection/2_round/results/1e-05_bs-gt-110_qcov-gt-80_len-200-1500/align/sirtuins_round-2_kingdom=euk_1e-05_bs-gt-110_qcov-gt-80_len-200-1500_50-80_rep_seq_19602-28711.fa similarity index 100% rename from dev/sirtuins/detection/2_round/results/1e-05_bs-gt-110_qcov-gt-80_len-200-1500/align/sirtuins_round-2_kingdom=euk_1e-05_bs-gt-110_qcov-gt-80_len-200-1500_50-80_rep_seq_19602-28711.fa rename to dev/sirtuins/1_detection/2_round/results/1e-05_bs-gt-110_qcov-gt-80_len-200-1500/align/sirtuins_round-2_kingdom=euk_1e-05_bs-gt-110_qcov-gt-80_len-200-1500_50-80_rep_seq_19602-28711.fa diff --git a/dev/sirtuins/detection/2_round/results/1e-05_bs-gt-110_qcov-gt-80_len-200-1500/mmseqs/sirtuins_round-2_kingdom=euk_1e-05_bs-gt-110_qcov-gt-80_len-200-1500_50-80_all_seqs.fasta b/dev/sirtuins/1_detection/2_round/results/1e-05_bs-gt-110_qcov-gt-80_len-200-1500/mmseqs/sirtuins_round-2_kingdom=euk_1e-05_bs-gt-110_qcov-gt-80_len-200-1500_50-80_all_seqs.fasta similarity index 100% rename from dev/sirtuins/detection/2_round/results/1e-05_bs-gt-110_qcov-gt-80_len-200-1500/mmseqs/sirtuins_round-2_kingdom=euk_1e-05_bs-gt-110_qcov-gt-80_len-200-1500_50-80_all_seqs.fasta rename to dev/sirtuins/1_detection/2_round/results/1e-05_bs-gt-110_qcov-gt-80_len-200-1500/mmseqs/sirtuins_round-2_kingdom=euk_1e-05_bs-gt-110_qcov-gt-80_len-200-1500_50-80_all_seqs.fasta diff --git a/dev/sirtuins/detection/2_round/results/1e-05_bs-gt-110_qcov-gt-80_len-200-1500/mmseqs/sirtuins_round-2_kingdom=euk_1e-05_bs-gt-110_qcov-gt-80_len-200-1500_50-80_cluster.tsv b/dev/sirtuins/1_detection/2_round/results/1e-05_bs-gt-110_qcov-gt-80_len-200-1500/mmseqs/sirtuins_round-2_kingdom=euk_1e-05_bs-gt-110_qcov-gt-80_len-200-1500_50-80_cluster.tsv similarity index 100% rename from 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similarity index 100% rename from dev/sirtuins/detection/2_round/results/1e-05_bs-gt-110_qcov-gt-80_len-200-1500/sirtuins_round-2_kingdom=euk_1e-05_bs-gt-110_qcov-gt-80_len-200-1500_domtblout.tsv rename to dev/sirtuins/1_detection/2_round/results/1e-05_bs-gt-110_qcov-gt-80_len-200-1500/sirtuins_round-2_kingdom=euk_1e-05_bs-gt-110_qcov-gt-80_len-200-1500_domtblout.tsv diff --git a/dev/sirtuins/detection/2_round/results/1e-05_bs-gt-110_qcov-gt-80_len-200-1500/sirtuins_round-2_kingdom=euk_1e-05_bs-gt-110_qcov-gt-80_len-200-1500_hits.faa b/dev/sirtuins/1_detection/2_round/results/1e-05_bs-gt-110_qcov-gt-80_len-200-1500/sirtuins_round-2_kingdom=euk_1e-05_bs-gt-110_qcov-gt-80_len-200-1500_hits.faa similarity index 100% rename from dev/sirtuins/detection/2_round/results/1e-05_bs-gt-110_qcov-gt-80_len-200-1500/sirtuins_round-2_kingdom=euk_1e-05_bs-gt-110_qcov-gt-80_len-200-1500_hits.faa rename to 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dev/sirtuins/detection/2_round/results/1e-05_bs-gt-110_qcov-gt-80_len-200-1500/sirtuins_round-2_kingdom=euk_domtblout.tsv rename to dev/sirtuins/1_detection/2_round/results/1e-05_bs-gt-110_qcov-gt-80_len-200-1500/sirtuins_round-2_kingdom=euk_domtblout.tsv diff --git a/dev/sirtuins/detection/2_round/results/1e-05_bs-gt-110_qcov-gt-80_len-200-1500/sirtuins_round-2_kingdom=euk_tblout.tsv b/dev/sirtuins/1_detection/2_round/results/1e-05_bs-gt-110_qcov-gt-80_len-200-1500/sirtuins_round-2_kingdom=euk_tblout.tsv similarity index 100% rename from dev/sirtuins/detection/2_round/results/1e-05_bs-gt-110_qcov-gt-80_len-200-1500/sirtuins_round-2_kingdom=euk_tblout.tsv rename to dev/sirtuins/1_detection/2_round/results/1e-05_bs-gt-110_qcov-gt-80_len-200-1500/sirtuins_round-2_kingdom=euk_tblout.tsv diff --git a/dev/sirtuins/detection/2_round/results/1e-05_bs-gt-20_qcov-gt-80_len-200-1500/align/sirtuins_round-2_kingdom=euk_1e-05_bs-gt-20_qcov-gt-80_len-200-1500_0.50-0.80_rep_seq.mafft.afa b/dev/sirtuins/1_detection/2_round/results/1e-05_bs-gt-20_qcov-gt-80_len-200-1500/align/sirtuins_round-2_kingdom=euk_1e-05_bs-gt-20_qcov-gt-80_len-200-1500_0.50-0.80_rep_seq.mafft.afa similarity index 100% rename from dev/sirtuins/detection/2_round/results/1e-05_bs-gt-20_qcov-gt-80_len-200-1500/align/sirtuins_round-2_kingdom=euk_1e-05_bs-gt-20_qcov-gt-80_len-200-1500_0.50-0.80_rep_seq.mafft.afa rename to dev/sirtuins/1_detection/2_round/results/1e-05_bs-gt-20_qcov-gt-80_len-200-1500/align/sirtuins_round-2_kingdom=euk_1e-05_bs-gt-20_qcov-gt-80_len-200-1500_0.50-0.80_rep_seq.mafft.afa diff --git a/dev/sirtuins/detection/2_round/results/1e-05_bs-gt-20_qcov-gt-80_len-200-1500/align/sirtuins_round-2_kingdom=euk_1e-05_bs-gt-20_qcov-gt-80_len-200-1500_0.50-0.80_rep_seq.muscle.afa b/dev/sirtuins/1_detection/2_round/results/1e-05_bs-gt-20_qcov-gt-80_len-200-1500/align/sirtuins_round-2_kingdom=euk_1e-05_bs-gt-20_qcov-gt-80_len-200-1500_0.50-0.80_rep_seq.muscle.afa similarity index 100% rename from dev/sirtuins/detection/2_round/results/1e-05_bs-gt-20_qcov-gt-80_len-200-1500/align/sirtuins_round-2_kingdom=euk_1e-05_bs-gt-20_qcov-gt-80_len-200-1500_0.50-0.80_rep_seq.muscle.afa rename to dev/sirtuins/1_detection/2_round/results/1e-05_bs-gt-20_qcov-gt-80_len-200-1500/align/sirtuins_round-2_kingdom=euk_1e-05_bs-gt-20_qcov-gt-80_len-200-1500_0.50-0.80_rep_seq.muscle.afa diff --git a/dev/sirtuins/detection/2_round/results/1e-05_bs-gt-20_qcov-gt-80_len-200-1500/align/sirtuins_round-2_kingdom=euk_1e-05_bs-gt-20_qcov-gt-80_len-200-1500_0_25871-32022.afa b/dev/sirtuins/1_detection/2_round/results/1e-05_bs-gt-20_qcov-gt-80_len-200-1500/align/sirtuins_round-2_kingdom=euk_1e-05_bs-gt-20_qcov-gt-80_len-200-1500_0_25871-32022.afa similarity index 100% rename from dev/sirtuins/detection/2_round/results/1e-05_bs-gt-20_qcov-gt-80_len-200-1500/align/sirtuins_round-2_kingdom=euk_1e-05_bs-gt-20_qcov-gt-80_len-200-1500_0_25871-32022.afa rename to dev/sirtuins/1_detection/2_round/results/1e-05_bs-gt-20_qcov-gt-80_len-200-1500/align/sirtuins_round-2_kingdom=euk_1e-05_bs-gt-20_qcov-gt-80_len-200-1500_0_25871-32022.afa diff --git a/dev/sirtuins/detection/2_round/results/1e-05_bs-gt-20_qcov-gt-80_len-200-1500/mmseqs/sirtuins_round-2_kingdom=euk_1e-05_bs-gt-20_qcov-gt-80_len-200-1500_0.50-0.80_all_seqs.fasta b/dev/sirtuins/1_detection/2_round/results/1e-05_bs-gt-20_qcov-gt-80_len-200-1500/mmseqs/sirtuins_round-2_kingdom=euk_1e-05_bs-gt-20_qcov-gt-80_len-200-1500_0.50-0.80_all_seqs.fasta similarity index 100% rename from dev/sirtuins/detection/2_round/results/1e-05_bs-gt-20_qcov-gt-80_len-200-1500/mmseqs/sirtuins_round-2_kingdom=euk_1e-05_bs-gt-20_qcov-gt-80_len-200-1500_0.50-0.80_all_seqs.fasta rename to dev/sirtuins/1_detection/2_round/results/1e-05_bs-gt-20_qcov-gt-80_len-200-1500/mmseqs/sirtuins_round-2_kingdom=euk_1e-05_bs-gt-20_qcov-gt-80_len-200-1500_0.50-0.80_all_seqs.fasta diff --git a/dev/sirtuins/detection/2_round/results/1e-05_bs-gt-20_qcov-gt-80_len-200-1500/mmseqs/sirtuins_round-2_kingdom=euk_1e-05_bs-gt-20_qcov-gt-80_len-200-1500_0.50-0.80_cluster.tsv b/dev/sirtuins/1_detection/2_round/results/1e-05_bs-gt-20_qcov-gt-80_len-200-1500/mmseqs/sirtuins_round-2_kingdom=euk_1e-05_bs-gt-20_qcov-gt-80_len-200-1500_0.50-0.80_cluster.tsv similarity index 100% rename from dev/sirtuins/detection/2_round/results/1e-05_bs-gt-20_qcov-gt-80_len-200-1500/mmseqs/sirtuins_round-2_kingdom=euk_1e-05_bs-gt-20_qcov-gt-80_len-200-1500_0.50-0.80_cluster.tsv rename to dev/sirtuins/1_detection/2_round/results/1e-05_bs-gt-20_qcov-gt-80_len-200-1500/mmseqs/sirtuins_round-2_kingdom=euk_1e-05_bs-gt-20_qcov-gt-80_len-200-1500_0.50-0.80_cluster.tsv diff --git a/dev/sirtuins/detection/2_round/results/1e-05_bs-gt-20_qcov-gt-80_len-200-1500/mmseqs/sirtuins_round-2_kingdom=euk_1e-05_bs-gt-20_qcov-gt-80_len-200-1500_0.50-0.80_rep_seq.fasta 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a/dev/sirtuins/detection/5_round_adl/results/1e-05_bs-gt-80_qcov-gt-60_len-100-2500/mmseqs/sir2_domain/sirtuins_round-5_kingdom=all_1e-05_bs-gt-80_qcov-gt-60_len-100-2500_hit_region_50-80_all_seqs.fasta b/dev/sirtuins/1_detection/5_round_adl/results/1e-05_bs-gt-80_qcov-gt-60_len-100-2500/mmseqs/sir2_domain/sirtuins_round-5_kingdom=all_1e-05_bs-gt-80_qcov-gt-60_len-100-2500_hit_region_50-80_all_seqs.fasta similarity index 100% rename from dev/sirtuins/detection/5_round_adl/results/1e-05_bs-gt-80_qcov-gt-60_len-100-2500/mmseqs/sir2_domain/sirtuins_round-5_kingdom=all_1e-05_bs-gt-80_qcov-gt-60_len-100-2500_hit_region_50-80_all_seqs.fasta rename to dev/sirtuins/1_detection/5_round_adl/results/1e-05_bs-gt-80_qcov-gt-60_len-100-2500/mmseqs/sir2_domain/sirtuins_round-5_kingdom=all_1e-05_bs-gt-80_qcov-gt-60_len-100-2500_hit_region_50-80_all_seqs.fasta diff --git 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