Tweaks to gene family README files

LEGUMES/Fabaceae/genefamilies/legume.fam1.M65K/README.mixed.fam1.M65K.yml

@@ -3,15 +3,22 @@ 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
+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: fabac
+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."
+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"
 

LEGUMES/Fabaceae/genefamilies/legume.fam3.VLMQ/README.fam3.VLMQ.yml

@@ -3,15 +3,30 @@ identifier: legume.fam3.VLMQ
 
 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
+synopsis: gene families and phylogenetic trees for the legume family; family set 3 calculated by the Legume Information System group
 
-scientific_name: legume
+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/legumeinfo/pandagma. 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 FastTree)."
+description: "Files in this directory include the main results for gene families constructed for the legume family.
+  Methods are documented at https://github.com/legumeinfo/pandagma. 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 FastTree).
+  The files labeled with 'base' are the primary gene families, calculated using 18 diverse legume taxa and three outgroup species.
+  The base files include, for each family: multifasta protein sets, initial alignments, hidden Markov models, alignments cleaned 
+  of indels (non-match state positions), and phylogenetic trees. The base families were calculated using pangene collections 
+  for six genera with good representation in terms of species and annotations (Arachis, Cicer, Glycine, Medicago, Phaseolus, Vigna),
+  while files labeled with 'sup1' consist of gene family sets for which selected species and annotations were placed into
+  the base families by homology. The gene families in the base and sup1 sets correspond by family name; for example,
+  Legume.fam3.01000 in the base files is the same family as Legume.fam3.01000 in sup1 (though containing different species sets).
+  The A and B sets (baseA, baseB; sup1A, sup1B) designate files (A) and directories/tar-balls (B). Each of the B tar-balls
+  can be extracted to produce a directory of approximately 25,000 gene family files of the indicated ty[e (proteomes, HMM models,
+  alignments, alignments trimmed of indels, and trees)."
 
 original_file_creation_date: "2024-02-27"
 
@@ -27,5 +42,6 @@ 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
+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