Updated Figure numbers in README

README.md

-# 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)