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legume.fam3.VLMQ.baseA_clust.tsv.gz: Gene family sets, in cluster format - i.e., ID in first column, followed by tab-separated gene list.
legume.fam3.VLMQ.baseA_counts.tsv.gz: Matrix of counts of genes per annotation set for each gene family.
legume.fam3.VLMQ.baseA_hsh.tsv.gz: Gene family file, in a two-column hash format, with the set ID in the first column and genes in the second.
legume.fam3.VLMQ.baseA_stats.txt: Descriptive statistics about program parameters, input sequences, and gene family products.
legume.fam3.VLMQ.baseA_table.tsv.gz: Tabular format of all gene families, in columns by species. Multiple paralogs from a species.
  in a gene family are comma-separated within the column of the species.

legume.fam3.VLMQ.baseB_proteomes.tar.gz: Directory with multifasta protein files for each gene family.
legume.fam3.VLMQ.baseB_aligns_prot.tar.gz: Directory with initial alignments of all family protein files.
legume.fam3.VLMQ.baseB_hmm.tar.gz: Hidden Markov Models (HMMs) calculated from all family alignments.
legume.fam3.VLMQ.baseB_hmmalign_trim.tar.gz: Trimmed alignments, from realignments of protein sequences against HMMs and non-match-states removed.
legume.fam3.VLMQ.baseB_trees.tar.gz: Phylogenetic trees calculated from trimmed alignments.

legume.fam3.VLMQ.sup1A_clust.tsv.gz: Gene family sets, in cluster format, for selected species placed into the base gene families by homology.
legume.fam3.VLMQ.sup1A_hsh.tsv.gz: Gene family sets, in two-column hash format, for selected species placed into the base gene families by homology.
legume.fam3.VLMQ.sup1A_counts.tsv.gz: Matrix of counts of genes per annotation set, with selected species placed into the base gene families by homology.
legume.fam3.VLMQ.sup1A_stats.txt: Gene family file, in a two-column hash format, for selected species placed into the base gene families by homology.
legume.fam3.VLMQ.sup1B_hmmalign_trim.tar.gz: Trimmed alignments, for selected species placed into the base gene families by homology.
legume.fam3.VLMQ.sup1B_proteomes.tar.gz: Directory with all family protein files, for selected species placed into the base gene families by homology.
legume.fam3.VLMQ.sup1B_trees.tar.gz: Phylogenetic trees calculated from trimmed alignments, for selected species placed into the base gene families by homology.