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…
☆49Updated 5 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☆46Updated 2 years ago
- Exploring the "dusk matter" of the RNA virosphere☆35Updated 3 years ago
- Binning Virus Genomes from Metagenomes☆66Updated 3 years ago
- Implementation of the TreeShrink problem☆50Updated last year
- Efficient phylogenetic tree inference for massive taxonomic datasets☆130Updated 6 months ago
- a UNIX shell toolkit for processing and analyzing multiple sequence alignments and phylogenies☆75Updated last month
- Fast and accurate tool for calculating Average Nucleotide Identity (ANI) and clustering virus genomes and metagenomes☆91Updated 5 months ago
- A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing☆69Updated 4 years ago
- Prediction of prophages from bacterial genomes☆81Updated 4 months ago
- all methods related to Enterobase☆43Updated last year
- A toolkit for exploring prokaryotic methylation and base modifications in nanopore sequencing☆50Updated last month
- Taxonomic classification of viruses at Order and Family level☆21Updated 2 years ago
- IQ-TREE version 3: software for phylogenetics☆80Updated this week
- Python code for versatile Functional Ontology Assignments for Metagenomes searching via Hidden Markov Model (HMM) with environmental focu…☆63Updated 2 weeks ago
- Phigaro is a scalable command-line tool for predicting phages and prophages☆53Updated last year
- Precise host read removal☆107Updated last month
- CLI tool to annotate genes with KOfam☆85Updated 2 years ago
- Program to quickly and accurately assemble plasmids in hybrid and long-only sequenced bacterial isolates☆78Updated last month
- EzAAI - High Throughput Prokaryotic AAI Calculator☆44Updated 2 months ago
- Improvement of metagenome-assembled genomes☆54Updated 5 years ago
- ☆72Updated 4 months ago
- Detection of pseudogene candidates in bacterial and archaeal genomes.☆51Updated last year
- From genomes to phenotypes: Traitar, the microbial trait analyzer☆61Updated 6 years ago
- A tool for drawing ANI clustermap between all-vs-all microbial genomes☆85Updated 5 months ago
- Collection of scripts for bacterial genomics☆48Updated 5 years ago
- Bifrost graph gene caller.☆95Updated last month
- viralVerify: viral contig verification tool