DATA PACKAGE FROM MORALES-BRIONES ET AL (American Journal of Botany)

Phylogenomic analyses using genomes and transcriptomes do not “resolve” relationships among major clades in Phrymaceae

This package contains the data and software outputs (i.e. fasta files, alignments, trees, etc).


1_transcriptomes_and_genomes:
	 final_filtered_transcriptomes: CDS and PEP Fasta files of filtered transcriptomes
	 genomes: Fasta files of CDS used genomes
	 original_transcriptome_assemblies: Fasta files of original Trinity transcriptome assemblies
2_final_homologs: Tree files of final homologs in newick format
3_MO_orthologs: Tree files of final MO orthologs in newick format
4_MO_fasta_files_24tx_aln: Alignment and clean Alignments in fasta format from MO orthologs.
5_concatenated_matrices: Concatenated alignment from 4_MO_fasta_files_24tx_aln in fasta, nexus and phylyip formats.
6_phylogenetic_analyses
	ASTRAL: Input and output files from ASTRAL
	IQtree_concatenated: Input and output files from IQ-Tree for the concatenated alignment.
	IQtree_invidivual_gene_trees: Input and output files from IQ-Tree for the individual MO ortholog alignments.
	IQtree_invidivual_gene_trees_rooted: Rooted trees in newick format from IQtree_invidivual_gene_trees
	Phyparts: Input and output files Phyparts
	QS: Input and output files from Quartet Sampling
	cpDNA: Analises of the chloroplast data set.
		 IQtree: Input and output files from IQ-Tree for the contiguous cpDNA alignment.
		 QS: Input and output files from Quartet Sampling
		 aln: Contiguous cpDNA alignment
		 assemblies: cpDNA assemblies using FastPlast
			 full_assemblies: Complete assemblies from 7 species.
			 partial_assemblies: Partial assemblies from 7 species.
	hybridization_test: Hybridization analyses
		 hyde: Input and output files from HyDe analyses.
		 phylonet: Input and output files from PhyloNet analyses.
			mcmc_gt: Input and output files from MCMC_GT analyses.
			ml: Input and output files from InferNetworks_ML analyses.
	map_dup: Input and output files from the orthogroup mapping.
	treepl: Input and output files from individual time-calibrated ortholog trees for cloudogram
	wgd: Input and output files from analyses of distribution of Synonymous Distance among Gene Pairs (Ks plots)
 
 
 If you have any question about the data, please do not hesitate to contact Diego F. Morales-Briones at dfmoralesb@gmail.com