LIS - Legume Information System
Information about legume traits for crop improvement
GlycineMine
v5.1.0.3
Glycine data from LIS
v5.1.0.3
Glycine data from LIS
| URL | https://data.legumeinfo.org/LEGUMES/Fabaceae/genefamilies/legume.genefam.fam1.M65K/ |
| 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. |
| Licence | ODC Public Domain Dedication and Licence (PDDL) |
| DataSource | LIS Datastore |
| Synopsis | gene families and phylogenetic trees for the legume family |
| Version | genefam.fam1 |
