Amalgamated likelihood estimation (ALE) is a probabilistic approach to exhaustively explore all reconciled gene trees that can be amalgamated as a combination of clades observed in a sample of gene trees. We implement the ALE approach in the context of a reconciliation model (cf. http://arxiv.org/abs/1211.4606 ), which allows for the duplication…
☆55May 14, 2025Updated last year
Alternatives and similar repositories for ALE
Users that are interested in ALE are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Helper scripts for making phylogenies☆15Jul 9, 2026Updated 2 months ago
- 📜 the Great Automatic Nomenclator — The Next Million Names for Archaea and Bacteria☆42Oct 28, 2025Updated 11 months ago
- Decomposition Into Single-COpy gene trees (DISCO) is a method for decomposing multi-copy gene-family trees while attempting to preserve o…☆13Jun 19, 2025Updated last year
- Scripts for calculating features and regression of prokaryote OGT☆26Feb 13, 2024Updated 2 years ago
- Drawing reconciled phylogenetic trees allowing 1, 2 or 3 reconcillation levels☆25Oct 24, 2025Updated 11 months ago
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- Gene tree - species tree reconciliation from gene tree distributions☆44Sep 14, 2026Updated 2 weeks ago
- ☆82May 2, 2026Updated 5 months ago
- Fast, accurate species tree estimation.☆13Aug 17, 2026Updated last month
- Estimate node ages of a phylogeny by approximating the phylogenetic likelihood with a multivariate normal distribution.☆12Jun 23, 2025Updated last year
- PhyloBayes: phylogenetic reconstruction using infinite mixtures (CAT and CAT-GTR) -- serial version (for MPI, see pbmpi.git)☆14Oct 21, 2021Updated 4 years ago
- ASTRAL for PaRalogs and Orthologs☆24Sep 13, 2022Updated 4 years ago
- ☆16Apr 11, 2026Updated 5 months ago
- A Swiss-Army-Knife for Bioinformaticians☆15Jul 26, 2026Updated 2 months ago
- Bayesian gene tree reconciliation and WGD inference using amalgamated likelihood estimation☆16Apr 29, 2025Updated last year
- AI Agents on DigitalOcean Gradient AI Platform • AdBuild production-ready AI agents using customizable tools or access multiple LLMs through a single endpoint. Create custom knowledge bases or connect external data.
- WITCH is a multiple sequence alignment method that uses multiple weighted HMMs to align unaligned sequences and find consensuses.☆13Nov 18, 2025Updated 10 months ago
- Python package for common tasks in bioinformatic.☆11Sep 24, 2025Updated last year
- SimPhy: A comprehensive simulator of gene family evolution☆36Jun 30, 2023Updated 3 years ago
- ☆68Oct 17, 2023Updated 2 years ago
- Protocol for finding informative protein families and then using them to score omic samples☆19Jul 27, 2022Updated 4 years ago
- A Python phyloinformatic toolkit, and an implementation of tree-heterogeneous models of evolution☆30Mar 11, 2026Updated 6 months ago
- orthology assignment using phylogenetic and network analyses☆57Updated this week
- DFAST Quality Control: Taxonomy and completeness check☆19Jun 17, 2026Updated 3 months ago
- MCMCtreeR: A package to estimate distribution values for temporal node constraints and prepare input files for MCMCtree☆46Nov 21, 2019Updated 6 years ago
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- Improving genome bins through the combination of different binning programs☆31Jan 30, 2023Updated 3 years ago
- PREQUAL: a pre-alignment quality filter for comparative sequence analyses☆34Jun 1, 2022Updated 4 years ago
- Phylogenetic penalized likelihood☆59Sep 8, 2026Updated 3 weeks ago
- Scripts and resources for analyzing sequence data for select eco-functional genes☆20May 25, 2017Updated 9 years ago
- Wrapper script to concatenate, align, and construct phylogenetic trees of BUSCOs☆20Sep 18, 2019Updated 7 years ago
- Horizontal gene transfer (HGT) identification pipeline☆70May 17, 2023Updated 3 years ago
- Structural and functional annotation of eukaryotic metagenome-assembled genomes☆24May 14, 2023Updated 3 years ago
- rapid phylogenomic tree calculator - A highly customizable framework for reproducible phylogenomic inference☆30Jul 1, 2026Updated 3 months ago
- GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.☆622Updated this week
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- ☆43Apr 2, 2024Updated 2 years ago
- Magnetosome gene cluster annotation, screening and visualization tool☆11Jul 2, 2025Updated last year
- A versatile and scalable algorithm for rogue taxon identification. Also includes implementations of the maximum agreement subtree, leaf s…☆23Aug 19, 2021Updated 5 years ago
- Discovery of conserved gene clusters in multiple genomes☆135Aug 21, 2026Updated last month
- RAxML Next Generation: faster, easier-to-use and more flexible☆478Sep 22, 2026Updated last week
- Microbial Phenotype Prediction, successor to PICA, implemented with Python 3.7 and scikit-learn☆13Sep 10, 2021Updated 5 years ago
- GenoVi, an automated customizable circular genome visualizer for bacteria and archaea☆110Jun 25, 2023Updated 3 years ago