ssolo / ALE
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…
☆46Updated 8 months ago
Alternatives and similar repositories for ALE:
Users that are interested in ALE are comparing it to the libraries listed below
- ☆70Updated last year
- A toolkit for exploring prokaryotic methylation and base modifications in nanopore sequencing☆44Updated 3 weeks ago
- A tool for generating consensus long-read assemblies for bacterial genomes☆97Updated last month
- a UNIX shell toolkit for processing and analyzing multiple sequence alignments and phylogenies☆67Updated 2 months ago
- Python code for versatile Functional Ontology Assignments for Metagenomes searching via Hidden Markov Model (HMM) with environmental focu…☆53Updated this week
- PANgenome with Annotations, COre identification, Tree and corresponding Alignments☆73Updated last year
- Binning Virus Genomes from Metagenomes☆60Updated 2 years ago
- PhyloFisher is a software package written in Python3 that can be used for the creation, analysis, and visualization of phylogenomic datas…☆31Updated last week
- A tool for drawing ANI clustermap between all-vs-all microbial genomes☆73Updated 5 months ago
- post processing of bacterial pangenome gene presence/absence matrices☆55Updated 5 months ago
- Program to quickly and accurately assemble plasmids in hybrid and long-only sequenced bacterial isolates☆60Updated last month
- EzAAI - High Throughput Prokaryotic AAI Calculator☆38Updated 4 months ago
- Classification of Eukaryotic and Prokaryotic sequences from metagenomic datasets☆69Updated 8 months ago
- Implementation of the TreeShrink problem☆38Updated 5 months ago
- IS mapping software☆53Updated 3 years ago
- A pipeline for running AMRfinderPlus and collating results into functional classes☆73Updated 6 months ago
- Inferring bacterial recombination rates from large-scale sequencing datasets.☆42Updated last year
- zol (& fai): large-scale targeted detection and evolutionary investigation of gene clusters (i.e. BGCs, phages, etc.)☆53Updated last week
- Bifrost graph gene caller.☆91Updated 5 months ago
- GTDB taxonomy taxdump files with trackable TaxIds☆52Updated 9 months ago
- lsaBGC - Lineage Specific Analysis of Biosynthetic Gene Clusters☆37Updated 6 months ago
- Detection of pseudogene candidates in bacterial and archaeal genomes.☆46Updated 10 months ago
- CLI tool to annotate genes with KOfam☆75Updated last year
- A tool for removing redundant genomes from a set of assemblies☆70Updated last year
- A tool for classifying prokaryote protein sequences into COG(Cluster of Orthologous Genes) functional category☆60Updated 5 months ago
- ☆52Updated 3 years ago
- FastOMA is a scalable software package to infer orthology relationship.☆70Updated this week
- Python tool to reduce size and redundancy of phylogenetic datasets☆31Updated last year
- From genomes to phenotypes: Traitar, the microbial trait analyzer☆57Updated 5 years ago
- A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing☆70Updated 3 years ago