Scripts and data associated with the publication on tree discordance and hybridization in the Petunia-Calibrachoa-Fabiana clade are available. Some data files are too large to be uploaded to Github; therefore, please refer to FigShare to download them. The raw transcriptome data were obtained from Wheeler et al. (2022) and (2023) and are deposited at SRA under BioProject PRJNA746328.
1. Correct reads with Rcorrector.
2. Remove adapters with Trimmomatic.
3. Map and index reads with BWA and SAMtools.
4. Call the most frequent base to obtain the consensus FASTA.
5. Combine the FASTA files from multiple individuals into a single FASTA file representing the genomic region/cluster/gene.
6. Align the FASTA files with MACSE.
7. Obtain gene trees with RAxML.
8. Estimate species tree with ASTRAL.
9. Assess ASTRAL tree discordance with Quartet Sampling.
10. Assess IQTree tree discordance with phyparts.
11. Estimate species tree with IQTree.
12 Assess IQTree tree discordance with ConcordanceFactors
13 Estimate species tree with SVDQuartets
14 Trim alignments to assess hybridization with HyDe.
15 Detect hybridization with HyDe.
16 Detect hybridization with QuiBL.
17 Calculate topology weight with Twisst.
18 Infer phylogenetic network with SNaQ.
19 Infer phylogenetic network with PhyloNet.
20 Calculate the likelihood of the PhyloNet networks.