Lists new analyses to README

README.md

@@ -1,4 +1,5 @@
-# Recurring adaptive introgression of a supergene that determines social organisation
+# Recurring adaptive introgression of a supergene variant that determines social organisation
+
 Eckart Stolle, Rodrigo Pracana, Marian K. Priebe, Gabriel Luis Hernández, Anurag Priyam, Federico López-Osorio, and Yannick Wurm
 
 ## Introduction
@@ -10,21 +11,23 @@ We genotyped a group of _Solenopsis_ samples, including _Solenopsis invicta_, _S
 
 ## Genotyping
 
-All steps relating to read filtering, mapping and genotype calling are presented in the directory `Genotyping`. This directory also includes the identification of single-copy genes with BUSCO.
+All steps relating to read filtering, mapping and genotype calling are presented in the directory [Genotyping](Genotyping). This directory also includes the identification of single-copy genes with BUSCO.
 
 ## Phylogenetic inferences
 
 We inferred the phylogenetic tree of the species and of the supergene using two different approaches:
-1. A coalescent-based approached detailed in the directory `Coalescence-based phylogenies`
-2. A concatenated alignment approach detailed in the directory `Phylogenies inferred with concatenated SNPs`
-
-A PCA of the supergene genotypes is presented in `PCA supergene SNPs` directory.
+1. A coalescent-based approached detailed in the directory [Coalescence-based phylogenies](Coalescence-based phylogenies)
+2. A concatenated alignment approach detailed in the directory [Phylogenies inferred with concatenated SNPs](Phylogenies inferred with concatenated SNPs)
+3. A dated phylogeny approach detailed in the directory [Dating divergence times](Dating divergence times)
+4. Quantification of introgression support using QuIBL [QuIBL analysis](QuIBL analysis)
+5. Topology weighting analysis using Twisst [Topology weighting](Topology weighting).
 
+A PCA of the supergene genotypes is presented in the directory [PCA supergene SNPs](PCA supergene SNPs).
 
 ## Nucleotide diversity
 
-See directory `Nucleotide diversity (pi)`.
+See directory [Nucleotide diversity (pi)](Nucleotide diversity (pi)).
 
 ## Bray-Curtis dissimilarity between haplotypes
 
-See directory `Bray-Curtis dissimilarity`.
+See directory [Bray-Curtis dissimilarity](Bray-Curtis dissimilarity).