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LegSF.fam3.W6TK.sup1A_clust.tsv: Gene family sets, in cluster format - i.e., ID in first column, followed by tab-separated gene list.
LegSF.fam3.W6TK.sup1A_counts.tsv: Matrix of counts of genes per annotation set for each gene family.
LegSF.fam3.W6TK.sup1A_hsh.tsv: Gene family file, in a two-column hash format, with the set ID in the first column and genes in the second.
LegSF.fam3.W6TK.sup1A_table.tsv: Tabular format of all gene families, in columns by species. Multiple paralogs from a species.
LegSF.fam3.W6TK.sup1A_stats.txt: Gene family file, in a two-column hash format, for selected species placed into the base gene families by homology.
LegSF.fam3.W6TK.sup1A_fam3_correspondence.clust.tsv: Correspondence between legume.fam3 families and LegSF.fam3 superfamilies, in cluster format
LegSF.fam3.W6TK.sup1A__fam3_correspondence.hsh.tsv: Correspondence between legume.fam3 families and LegSF.fam3 superfamilies, in hash format

LegSF.fam3.W6TK.sup1B_hmm: Hidden Markov Models (HMMs) calculated from all family alignments.
LegSF.fam3.W6TK.sup1B_hmmalign: Directory of protein alignments, against HMMs
LegSF.fam3.W6TK.sup1B_hmmalign_trim: Trimmed alignments, from realignments of protein sequences against HMMs and non-match-states removed.
LegSF.fam3.W6TK.sup1B_proteomes: Directory with all family protein files, for selected species placed into the base gene families by homology.
LegSF.fam3.W6TK.sup1B_trees: Phylogenetic trees calculated from trimmed alignments, for selected species placed into the base gene families by homology.