ssolo / ALELinks
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…
☆48Updated 3 months ago
Alternatives and similar repositories for ALE
Users that are interested in ALE are comparing it to the libraries listed below
Sorting:
- Python tool to reduce size and redundancy of phylogenetic datasets☆45Updated 2 years ago
- a UNIX shell toolkit for processing and analyzing multiple sequence alignments and phylogenies☆74Updated 3 weeks ago
- Python code for versatile Functional Ontology Assignments for Metagenomes searching via Hidden Markov Model (HMM) with environmental focu…☆59Updated 4 months ago
- Prediction of prophages from bacterial genomes☆79Updated 2 months ago
- Efficient phylogenetic tree inference for massive taxonomic datasets☆124Updated 4 months ago
- A toolkit for exploring prokaryotic methylation and base modifications in nanopore sequencing☆49Updated 2 months ago
- CLI tool to annotate genes with KOfam☆86Updated 2 years ago
- Follow up to Grace Blackwell's 661k dataset, for 2023☆115Updated last week
- Fast and accurate tool for calculating Average Nucleotide Identity (ANI) and clustering virus genomes and metagenomes☆88Updated 3 months ago
- Implementation of the TreeShrink problem☆47Updated 11 months ago
- Exploring the "dusk matter" of the RNA virosphere☆35Updated 3 years ago
- A toolkit for prokaryotic comparative genomics☆50Updated 7 months ago
- ☆72Updated 3 months ago
- Binning Virus Genomes from Metagenomes☆66Updated 3 years ago
- Program to quickly and accurately assemble plasmids in hybrid and long-only sequenced bacterial isolates☆73Updated 2 months ago
- tiara – a tool for DNA sequence classification☆67Updated last year
- IQ-TREE version 3: software for phylogenetics☆68Updated 2 weeks ago
- EzAAI - High Throughput Prokaryotic AAI Calculator☆44Updated last month
- BRIG is a cross-platform (Windows/Mac/Unix) application that can display circular comparisons between a large number of genomes, with a f…☆36Updated 6 years ago
- zol (& fai): large-scale targeted detection and evolutionary investigation of gene clusters (i.e. BGCs, phages, etc.)☆62Updated this week
- Microbial Populations as Clusters Of Gene Transfer☆44Updated last year
- PHANOTATE: a gene caller for phages.☆78Updated 9 months ago
- A Python library that exposes features from IQ-TREE - efficient software for phylogenomic inference☆34Updated last week
- Bifrost graph gene caller.☆96Updated 11 months ago
- A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing☆70Updated 4 years ago
- PANgenome with Annotations, COre identification, Tree and corresponding Alignments☆74Updated last year
- A workflow and scripts for large-scale antiSMASH analyses☆41Updated 4 months ago
- Phigaro is a scalable command-line tool for predicting phages and prophages☆52Updated last year
- FastOMA is a scalable software package to infer orthology relationship.☆79Updated this week
- Strain resolver for metagenomics☆79Updated last year