From 52650cc0739bff2d400db0e4f9170105e9a068e3 Mon Sep 17 00:00:00 2001 From: Hugo VAYSSET <hvaysset@maestro-submit.maestro.pasteur.fr> Date: Sun, 30 Mar 2025 11:44:59 +0200 Subject: [PATCH] Updated Figure numbers in README --- README.md | 30 +++++++++++++++--------------- 1 file changed, 15 insertions(+), 15 deletions(-) diff --git a/README.md b/README.md index 353511b..bb7f930 100644 --- a/README.md +++ b/README.md @@ -1,21 +1,21 @@ -# SIRanc +# SIRal -Phylogenetic analyses related with the evolutionary history of SIRanc (FAM118B) and SIRim proteins. +Phylogenetic analyses related with the evolutionary history of SIRal (FAM118B) and SIRim proteins. -Bonhomme, Vaysset, Ednacot, Rodrigues, Cury, Hernandez Trejo, Benaroch, Morehouse, Bernheim & Poirier (2024). +Bonhomme*, Vaysset*, Ednacot, Rodrigues, Saloum, Cury, Benchetrit, Hernandez Trejo, Vittot, Bories, Levraud, Hernandez, Benaroch, Morehouse, Bernheim & Poirier (2024). ### Directory -- `dev/initial_mixed_detection` : Initial detection of SIR2 subfamily and SIRim proteins (data not shown) +- `dev/phylo_sir2_sirim` : Joint phylogeny of SIR2 and SIRim subfamily proteins (Figure 1a) - `dev/minimal_alignment` : Alignment of a subsample of SIR2 and SIRim subfamily proteins (Figure S2) -- `dev/sirim/1_detection` : Detection of SIRim subfamily proteins (Used in all phylogenetic analyses) -- `dev/sirim/2_align` : Alignment of SIRim subfamily proteins -- `dev/sirim/3_phylo_sirim_domain`: Phylogeny of SIRim subfamily proteins (Figure 4a) -- `dev/sirim/3.1_additional_trees`: Phylogeny of SIRim subfamily proteins (Figure S7) -- `dev/sirim/3.2_phylo_full_protein`: Phylogeny of SIRim subfamily proteins -- `dev/sirim/3.3_phylo_euk`: Phylogeny of SIRim subfamily proteins (Figure S6, S8) -- `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 (Figure S1) -- `dev/sirim/5_focus_eukaryotes` : Analyses regaring clades of eukaryotic SIRim (Figure 4, Figures S6-S8) -- `dev/sirim/5_focus_eukaryotes/clade_<ID>/structures` : AlphaFold2 models present in Figure 4b. +- `dev/sirim` : Analyses focusing of the SIRIm subfamily (detection, phylogeny, focus on eukaryotic sirims...) + - `dev/sirim/1_detection` : Detection of SIRim subfamily proteins (Used in all phylogenetic analyses) + - `dev/sirim/2_align` : Alignment of SIRim subfamily proteins + - `dev/sirim/3_phylo_sirim_domain`: Phylogeny of SIRim subfamily proteins (Figure 4a) + - `dev/sirim/3.1_additional_trees`: Phylogeny of SIRim subfamily proteins (Figure S6) + - `dev/sirim/3.2_phylo_full_protein`: Phylogeny of SIRim subfamily proteins + - `dev/sirim/3.3_phylo_euk`: Phylogeny of SIRim subfamily proteins (Figure S5, S7) + - `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 (Figure S1) + - `dev/sirim/5_focus_eukaryotes` : Analyses regaring clades of eukaryotic SIRim (Figure 4, Figures S5-S7) + - `dev/sirim/5_focus_eukaryotes/clade_<ID>/structures` : AlphaFold2 models present in Figure 4b. - `dev/sirtuins/1_detection` : Detection of SIR2 subfamily proteins (Used in all phylogenetic analyses) -- `dev/phylo_sir2_sirim` : Joint phylogeny of SIR2 and SIRim subfamily proteins (Figure 1a) - +- `dev/initial_mixed_detection` : Initial detection of SIR2 subfamily and SIRim proteins (data not shown) -- GitLab