Each step is an independent function. Run the full pipeline, specific ranges, or individual steps.
Fetches the seed HMM by PFam accession, or uses a locally supplied model file, as the starting point for the search.
HMM search, protein filtering, domain extraction, alignment, and model adjustment with WebLogo generation.
Repeats mining with the species-specific model to capture additional members missed by the raw PFam model.
De novo identification of conserved protein motifs across all family members.
Maps exon/intron boundaries for each family member from the genome annotation.
Extracts upstream promoter sequences and tests them for transcription-factor binding motif enrichment against JASPAR with FIMO/AME.
Scans the genome for degenerate, non-functional copies of the gene family missed by protein-based mining.
CDS extraction, nucleotide alignment, and maximum-likelihood tree inference with IQ-TREE, with optional bootstrapping.
Combines the tree, domain architecture, gene structure, MEME motifs, and cis-element hits into one publication-ready figure.
Molecular weight, isoelectric point, GRAVY index, and other protein properties for all family members.
Predicts subcellular localization for each protein with WoLF PSORT.
Identifies tandem and segmental duplications with MCScanX, computes Ka/Ks ratios, and renders a circos-style synteny plot.
Compiles every step's outputs into a single, publication-ready summary report for the family.
Run the entire pipeline with a single command.