Paper: Buxus and Tetracentron genomes help resolve eudicot phylogeny, ancient polyploidy, and paleogenomes

Authors: Andre S. Chanderbali1, Lingling Jin, Qiaoji Xu, Yue Zhang, Jingbo Zhang, Shuguang Jian, Emily Carroll, David Sankoff, Victor A. Albert, Dianella G. Howarth, Douglas E. Soltis and Pamela S. Soltis

Description:

This README file describes the data package accompanying the above publication. 

Files are organized by analysis in four main archives:

Genome_Assemblies.tar
	Buxus_sinica.genome.zip: 
		Buxus_sinica_v1.0.genome.fasta. 	#Genome assembly fasta file
		Buxus_sinica_v1.0.gff 			#annotation file in gff format
		Buxus_sinica_v1.0.cds.fasta 		#predicted coding sequences
		Buxus_sinica_v1.0.pep.fasta 		#predicted protein sequences
	Tetracentron_sinense.genome.zip:
		Tetracentron_sinense_v1.0.genome.fasta 	#Genome assembly fasta file
		Tetracentron_sinense_v1.0.gff 		#annotation file in gff format
		Tetracentron_sinense_v1.0.cds.fasta 	#predicted coding sequences
		Tetracentron_sinense_v1.0.pep.fasta 	#predicted protein sequences


Species_phylogenomics.tar
	353_loci.zip*					#alignments and RAxML output file for each Angiosperms353 locus
	353_supermatrix.zip**				#supermatrices of aligned Angiosperms353 loci, partition information, and RAxML and MrBayes output files
	Busco_loci.zip*					#alignments and RAxML output files for each BUSCO locus
	Busco_supermatrix.zip**				#supermatrices of aligned BUSCO loci, partition information, and RAxML and MrBayes output files
	Orthogroups.zip***		 		#alignments and IQ-TREE output files for each orthogroup
	 

Subgenome_phylogenomics.tar
	Ancestral_Chromosome_1.zip*			#alignments and RAxML output files for Ancestral_Chromosome_1 syntelogs
	Ancestral_Chromosome_2.zip*			#alignments and RAxML output files for Ancestral_Chromosome_2 syntelogs
	Ancestral_Chromosome_3.zip*			#alignments and RAxML output files for Ancestral_Chromosome_3 syntelogs
	Ancestral_Chromosome_4.zip*			#alignments and RAxML output files for Ancestral_Chromosome_4 syntelogs
	Ancestral_Chromosome_5.zip*			#alignments and RAxML output files for Ancestral_Chromosome_5 syntelogs
	Ancestral_Chromosome_6.zip*			#alignments and RAxML output files for Ancestral_Chromosome_6 syntelogs
	Ancestral_Chromosome_7.zip*			#alignments and RAxML output files for Ancestral_Chromosome_7 syntelogs


Ancestral_Genomes.tar
	GO_Annotations					#GO annotations for loci placed on ancestral genomes
	Reconstructions					#ordered arragement of loci on ancestral genomes

*RAxML output files include RAxML_bestTree, RAxML_bipartitionsBranchLabels, RAxML_bipartitions, RAxML_bootstrap, and RAxML_info written for each MSA
**MrBayes output files .ckp, .con.tre, .log.txt, .mcmc, .parts. .pstat, .p, .t, .trprobs, .tstst, and .vstat files written for each MSA
***IQ-TREE output files include .bionj, .ckp.gz, .contree, .iqtree, .log, .mldist, .model.gz, .splits.nex, and .treefile written for each MSA