---
identifier: legume.genefam.fam1.M65K

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 families and phylogenetic trees for the legume family; family set 1 calculated by the Legume Information System group

scientific_name: Fabaceae

scientific_name_abbrev: legume

taxid: 3803

description: "Files in this directory include the main results for gene families constructed for the legume family.
  Methods are documented at https://github.com/LegumeFederation/legfed_gene_families. Briefly, the methods are based
  on gene pairs filtered for per-species Ks values. These were clustered using Markov clustering. Sequence match scores
  of each sequence in a family were used to identify outliers, on the basis of score value relative to the median score
  for the family. Remaining sequences were re-clustered, added to the HMM set. Then all sequences were searched against
  all HMMs, realigned, re-screened relative to median match score, and finally used to generate alignments and phylogenetic
  trees (using RAxML). The trees are rooted, when possible, using the closest outgroup from among five outgroup species:
  Arabidopsis thaliana, Prunus persica, Cucumis sativa, Solanum lycopersicum, and Vitis vinifera."

original_file_creation_date: "2018-03-21"

local_file_creation_date: "2018-03-23"

dataset_release_date: "2018-03-23"

publication_doi: 10.3389/fpls.2019.00345

contributors: "Steven Cannon, David Fernandez-Baca, Akshay Yadav, Jacob Stai, Andrew Farmer, Carole Sinou, Anne Bruneau"

citation: "Stai JS, Yadav A, Sinou C, Bruneau A, Doyle JJ, Fernández-Baca D, Cannon SB. Cercis: A Non-polyploid Genomic Relic Within the Generally Polyploid Legume Family. Front Plant Sci. 2019 Apr 11;10:345. doi: 10.3389/fpls.2019.00345. PMID: 31105714; PMCID: PMC6499179."

data_curators: Steven Cannon

public_access_level: public

license: open

keywords: legumes, gene family, Glycine max, Phaseolus vulgaris, Vigna angularis, Vigna radiata, Vigna unguiculata, Cajanus cajan, Medicago truncatula, Cicer arietinum, Trifolium pratense, Lotus japonicus, Lupinus angustifolius, Arachis duranensis, Arachis ipaensis, Arachis hypogaea