A curated list of resources for using LLMs to develop more competitive grant applications.

Gene tree - species tree reconciliation from gene tree distributions

A telomere-to-telomere toolkit for gap-free genome assembly and centromeric repeat identification

RepeatIdentifier

Centromics: visualing centromeres with multiple omics data

Earl Grey: A fully automated TE curation and annotation pipeline

PHAST

The dynamics of chromosome evolution in the Malvaceae.

PLMAlign utilizes per-residue embeddings as input to obtain specific alignments and more refined similarity

PLMSearch enables accurate and fast homologous protein search with only sequences as input

Long-reads Gap-free Chromosome-scale Assembler

horIzoNtal TransfER CHAracterization in Non-assembled GEnome

Gene Family Annotation Workflow

A tool to assign ancestral linkage units and/or identify fusion/fission events in Lepidopteran chromosomes based on a set of reference BUSCO genes as markers.

Hierarchical Alignment Format

Detecting multi-genome synteny using minimizer graph mapping

Application of pan-genome for population

a lightweight bam file depth statistical tool

SYNPHONI is a tool designed for reconstructing the dynamic evolution of syntenic relationships across all scales of phylogenetic distance and genome organization. It thus provides a syntenic comple…

Library of usual classes and functions written in python and used in the Dyogen team for comparative genomics applications

SCORPiOs is a synteny-guided gene tree correction pipeline for clades that have undergone a whole-genome duplication event.

Foreign Contamination Screening caller scripts and documentation

A genome-scale, fast, and precise segmental duplications mapping tool