Improved Inference of Ortholog Groups using Hidden Markov Models
☆38Sep 14, 2025Updated 5 months ago
Alternatives and similar repositories for orthohmm
Users that are interested in orthohmm are comparing it to the libraries listed below
Sorting:
- a broadly applicable tool for automated gene identification and retrieval☆40Feb 22, 2026Updated 2 weeks ago
- PSAURON is a machine learning model for rapid assessment of protein coding gene annotation☆54Dec 11, 2025Updated 2 months ago
- An R package to identify and classify duplicated genes from whole-genome protein sequence data☆32Sep 11, 2025Updated 5 months ago
- BOSTIn is a new, user-friendly phylogenetic artifact identification package.☆11Jan 20, 2026Updated last month
- pangenome from maximal blocks in an MSA☆11Sep 17, 2024Updated last year
- a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference☆86Feb 27, 2026Updated last week
- ☆17Mar 2, 2024Updated 2 years ago
- Codon-Aware Multiple Sequence Alignments☆20Nov 15, 2024Updated last year
- Fast long-read mapper and whole-genome aligner (accelerated version of minimap2)☆43Jan 7, 2026Updated 2 months ago
- Quartet-based species tree and tree of blob estimation☆14Feb 10, 2026Updated last month
- GALBA is a pipeline for fully automated prediction of protein coding gene structures with AUGUSTUS in novel eukaryotic genomes for the sc…☆148Jan 27, 2025Updated last year
- The Dagstuhl Format for Assembly☆13Oct 16, 2017Updated 8 years ago
- Tool for fully-automated inference of species trees from raw genome assemblies☆44Feb 15, 2026Updated 3 weeks ago
- Multi-genome synteny block visualization tool☆55Mar 3, 2026Updated last week
- A database for signatures of public genomic sources☆18Jan 1, 2026Updated 2 months ago
- Compute various quantitative genetics parameters from a Generalised Linear Mixed Model (GLMM) estimates. Especially, it yields the observ…☆16Jan 20, 2025Updated last year
- a tree splitting and pruning algorithm for retrieving single-copy orthologs from gene family trees☆29Feb 23, 2026Updated 2 weeks ago
- Detecting multi-genome synteny using minimizer graph mapping☆103Feb 9, 2026Updated last month
- Two-dimensional outlier detection algorithm for pinpointing errors in small species-specific stretches of the multiple sequence alignment…☆16May 27, 2024Updated last year
- ☆16Feb 20, 2024Updated 2 years ago
- Code to perform homolog detectability analyses as described in Weisman et al. 2020 (https://www.biorxiv.org/content/10.1101/2020.02.27.96…☆18Nov 18, 2024Updated last year
- Taxon-aware analysis of clustered protein sequences☆31Jul 1, 2024Updated last year
- Tiberius is a deep learning gene finder.☆99Feb 26, 2026Updated last week
- a UNIX shell toolkit for processing and analyzing multiple sequence alignments and phylogenies☆82Mar 3, 2026Updated last week
- biodiversity genomics course by Nicol Rueda, Karin Näsvall, Fernando Seixas and Joana Meier from the Wellcome Sanger Institute☆68Feb 21, 2026Updated 2 weeks ago
- Remove contaminated contigs from genomes using k-mers and taxonomies.☆60Nov 3, 2023Updated 2 years ago
- 🚀 LiftOn: Accurate annotation mapping for GFF/GTF across assemblies☆122Feb 24, 2026Updated 2 weeks ago
- rnalib: a python-based transcriptomics library☆11Jan 23, 2026Updated last month
- A local-haplotagging-based small and structural variant caller☆95Feb 27, 2026Updated last week
- reference-free estimation of ploidy level from whole genome sequencing data based on de Bruijn graph☆18Jul 26, 2023Updated 2 years ago
- A tool to calculate ploidy levels from genotype likelihoods and coverage using Hidden Markov Models☆18Nov 29, 2022Updated 3 years ago
- Annotated Genome Optimization Using Transcriptome Information☆20May 31, 2020Updated 5 years ago
- Long-read splice alignment with high accuracy☆64Sep 26, 2024Updated last year
- DNA assembler developed on FER (Croatia), RBI (Croatia) and GIS (Singapore)☆18Jan 18, 2016Updated 10 years ago
- BigSeqKit: a parallel Big Data toolkit to process FASTA and FASTQ files at scale☆57Aug 6, 2023Updated 2 years ago
- This pipeline is used to distinguish allotetraploid subgenomes.☆11Apr 8, 2024Updated last year
- Constructing a pangenome gene graph☆204Aug 11, 2025Updated 6 months ago
- Long-read Isoform Quantification and Analysis☆38Mar 25, 2025Updated 11 months ago
- Merging assemblies by using adjacency algebraic model and classification☆22Jun 17, 2023Updated 2 years ago