Tremble_et_al_2023_BoletaceaePhylogeny.zip

This folder contains all gene alignments produced by mafft, gene trees produced by iqtree2, and coalescent species tree produced by astral.
File Descriptions:
Boletaceae_allBUSCO_astral-hybrid_summaryCoalescent.BS10_branchDropped.paxillusRoot.tre = This is the summary coalescent phylogeny produced by astral hybrid from all BUSCO genes used in the study, and is rooted with Paxillus.
Boletaceae_allBUSCO_astral-hybrid_summaryCoalescent.BS10_branchDropped.tre = This is the unrooted summary coalescent phylogeny produced by astral hybrid from all BUSCO genes used in the study.
Boletaceae_allBUSCO_concatenatedSupermatrix.mafft.fasta.gz = Alignment of all BUSCO genes concatenated.
Boletaceae_allBUSCO_concatenatedSupermatrix.partitions.txt.gz = Partitions of all BUSCO gene concatenated dataset.
Boletaceae_allBUSCO_concatenatedSupermatrix.treefile = Summary coalsecent phylogeny with branch lengths estimated with IQtree using the above concatenated dataset.
alignments/ = BUSCO gene alignments with specimenID and geneID in fasta header.
alignments_noGeneName/ = BUSCO gene alignments with only specimenID in fasta header
raw_genes/ = unaligned BUSCO genes with specimenID and geneID in fasta header.
treefiles/ = individual gene trees produced from BUSCO genes with iqtree2