datamonkey/hyphaeon

doubletrouble aims to identify duplicated genes from whole-genome protein sequences and classify them based on their modes of duplication. The duplication modes are i. segmental duplication (SD); ii. tandem duplication (TD); iii. proximal duplication (PD); iv. transposed duplication (TRD) and; v. dispersed duplication (DD). Transposon-derived duplicates (TRD) can be further subdivided into rTRD (retrotransposon-derived duplication) and dTRD (DNA transposon-derived duplication). If users want a simpler classification scheme, duplicates can also be classified into SD- and SSD-derived (small-scale duplication) gene pairs. Besides classifying gene pairs, users can also classify genes, so that each gene is assigned a unique mode of duplication. Users can also calculate substitution rates per substitution site (i.e., Ka and Ks) from duplicate pairs, find peaks in Ks distributions with Gaussian Mixture Models (GMMs), and classify gene pairs into age groups based on Ks peaks.

A local command-line tool for ancestral sequence reconstruction with gap-state inference using IQ-TREE. It supports nucleotide, amino acid, and codon sequence alignments and reports site-wise posterior probabilities of ancestral states.

🧬 BioReason-ProAdvancing Protein Function Prediction withMultimodal Biological Reasoning

OmniTCR is a component-aware autoregressive foundation model for learning relationships among peptide epitopes, major histocompatibility complex (MHC) molecules, T-cell receptor alpha chains (TRA) and T-cell receptor beta chains (TRB).

GeneLinguaLM is a multimodal model that generates natural language descriptions of protein functions from amino acid sequences.

gemma4-12b-bioinfo is a fine-tuned Gemma 4 12B instruction model for bioinformatics, genomics, and computational biology question answering.