---
identifier: LegSF.fam3.W6TK

provenance: "The files in this directory are considered the primary instancess. The files here are held as part of the LegumeFederation and associated projects, e.g. LegumeInfo, PeanutBase, etc."

synopsis: gene superfamilies and phylogenetic trees generally spanning angiosperm evolution, including a set of diverse legume species and six nonlegume dicots

scientific_name: Fabaceae

scientific_name_abbrev: legume

taxid: 3803

description: "Files in this directory include gene superfamilies based on the legume.fam3 gene families.
  For each of the legume.fam3, a consensus sequence was calculated; then these were used as inputs to
  mmseqs easy-cluster, with min-seq-id=0.40, coverage=0.50, cov-mode 0.
  This produces a file of pairs of legume gene family IDs with homology above the specified cutoffs.
  That file of homology pairs was then clustered using Markov clustering (mcl), with inflation 1.6.
  Given those clusters of legume family IDs, sequences comprising those families were retrieved into 
  14904 superfamily proteome files. Each of those superfamily multifasta files was then aligned and used
  to create a superfamily HMM. Those HMMs were then used as targets for hmmsearch to place proteins 
  from each of 18 selected species (6 non-legume outgroup species and 12 diverse legume species) into the
  best-matching superfamily."

original_file_creation_date: "2025-06-11"

local_file_creation_date: "2025-06-11"

dataset_release_date: "2025-08-06"

contributors: "Steven Cannon, Hyunoh Lee"

data_curators: Steven Cannon

public_access_level: public

license: open

keywords: legumes, angiosperms, gene superfamily, Aeschynomene evenia, Arabidopsis thaliana, 
  Bauhinia variegata, Cercis canadensis, Chamaecrista fasciculata, Glycine max, Lotus japonicus, 
  Medicago truncatula, Parasponia andersonii, Phanera championii, Phaseolus vulgaris, Prunus persica, 
  Quillaja saponaria, Senna tomentosa, Sindora glabra, Trema orientale, Vitis vinifera