Phylogram

legfed_v1_0.L_1X7X83: GATA type zinc finger transcription factor family protein; IPR001781 (Zinc finger, LIM-type); GO:0008270 (zinc ion binding)

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Cross References

legfed_v1_0.L_1X7X83: GATA type zinc finger transcription factor family protein; IPR001781 (Zinc finger, LIM-type); GO:0008270 (zinc ion binding)

DatabaseAccession
legfed_v1_0 legfed_v1_0.L_1X7X83
Analysis

legfed_v1_0.L_1X7X83: GATA type zinc finger transcription factor family protein; IPR001781 (Zinc finger, LIM-type); GO:0008270 (zinc ion binding)

NameDescriptionMetadata
legfed_v1_0The gene families at LegumeInfo were calculated as part of the NSF LegumeFederation project, as follows (to be described in more detail in a paper anticipated for late 2018). Clustering was done on the basis of 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.legfed_v1_0 null 2017-10-17 01:03:47.320672