Issues

• Add the fungtion module for fungal effectors prediction

  enhancement
  Enhancement

  nf-core/proteinannotator#104 · Filter by author vagkaratzas opened on Jul 2, 2026

• Add the caalm module for cazyme annotation

  enhancement
  Enhancement

  nf-core/proteinannotator#94 · Filter by author vagkaratzas opened on May 5, 2026
  1

• Add TM-Vec and DeepBLAST from "Protein remote homology detection and structural alignment using deep learning"

  enhancement
  nf-core/proteinannotator#38 · Filter by author olgabot opened on May 13, 2025

• Add mTM-Align

  enhancementnf-core module
  nf-core/proteinannotator#37 · Filter by author olgabot opened on May 13, 2025
  2

  

• Add S2F (Sequence to Function) from "Protein function prediction for newly sequenced organisms"

  enhancement
  nf-core/proteinannotator#36 · Filter by author olgabot opened on May 13, 2025

• Add REBEAN (Read Embedding Based Enzyme Annotator) from "Deciphering enzymatic potential in metagenomic reads through DNA language model"

  enhancement
  nf-core/proteinannotator#35 · Filter by author olgabot opened on May 13, 2025

• Add ProtTucker from "Contrastive learning on protein embeddings enlightens midnight zone"

  enhancement
  nf-core/proteinannotator#33 · Filter by author olgabot opened on May 13, 2025

• Add PLMsearch from "PLMSearch: Protein language model powers accurate and fast sequence search for remote homology"

  enhancement
  nf-core/proteinannotator#32 · Filter by author olgabot opened on May 13, 2025

• Add MMseqs

  enhancementnf-core module
  nf-core/proteinannotator#31 · Filter by author olgabot opened on May 13, 2025
  2

  

• Add dense homolog retriever (DHR) from "Fast, sensitive detection of protein homologs using deep dense retrieval"

  enhancement
  nf-core/proteinannotator#29 · Filter by author olgabot opened on May 13, 2025

• Add CLEAN (contrastive learning-enabled enzyme annotation) from "Functional protein mining with conformal guarantees"

  enhancement
  nf-core/proteinannotator#28 · Filter by author olgabot opened on May 13, 2025

• Add BLAST/BLASTP

  enhancementnf-core module
  nf-core/proteinannotator#27 · Filter by author olgabot opened on May 13, 2025
  

• Add FANTASIA (recommended by Earth Biogenome Project)

  enhancement
  Enhancement

  nf-core/proteinannotator#25 · Filter by author olgabot opened on Apr 23, 2025

• Add EnTAP (recommended by Earth Biogenome Project)

  enhancement
  nf-core/proteinannotator#24 · Filter by author olgabot opened on Apr 23, 2025

• Add ProtNote

  enhancement
  nf-core/proteinannotator#22 · Filter by author olgabot opened on Apr 21, 2025

• Add protein disorder calculation

  enhancement
  nf-core/proteinannotator#19 · Filter by author olgabot opened on Mar 30, 2025

• Add EggnogMapper

  enhancement
  nf-core/proteinannotator#16 · Filter by author olgabot opened on Mar 26, 2025
  1

  

• Aggregate annotations across tools

  enhancement
  nf-core/proteinannotator#8 · Filter by author olgabot opened on Mar 24, 2025

• Add UniProt's UniFire

  enhancement
  nf-core/proteinannotator#4 · Filter by author olgabot opened on Mar 24, 2025
  1

  

• Add DIAMOND-Blastp

  enhancement
  nf-core/proteinannotator#2 · Filter by author olgabot opened on Mar 24, 2025