songweizhi / HgtSIMLinks
A simulator for horizontal gene transfer (HGT) in microbial communities
☆9Updated 4 years ago
Alternatives and similar repositories for HgtSIM
Users that are interested in HgtSIM are comparing it to the libraries listed below
Sorting:
- An R package identifying horizontal gene co-transfer between bacteria using association analysis and whole-genome sequences☆25Updated 2 years ago
- Calculate assocations between genes and traits☆23Updated 2 months ago
- a pipeline for reconciliation of phylogenetic histories within a bacterial pangenome☆49Updated 2 years ago
- Please use mmgenome2 instead. Tools for extracting individual genomes from metagenomes☆27Updated 7 years ago
- Improvement of metagenome-assembled genomes☆52Updated 5 years ago
- Automated strain separation of low-complexity metagenomes☆51Updated 3 years ago
- SCAPP is a plasmid assembly tool. This tool is described in our paper: https://microbiomejournal.biomedcentral.com/articles/10.1186/s4016…☆30Updated 2 years ago
- MetaGeneMark-2: Improved Gene Prediction in Metagenomes☆21Updated last year
- SynTracker is a pipeline, designated to determine the biological relatedness of conspecific strains (microbial strains of the same specie…☆29Updated 4 months ago
- skDER & CiDDER: efficient & high-resolution dereplication of microbial genomes.☆45Updated last week
- A Python implementation of the OrthoANI algorithm for nucleotide identity measurement.☆25Updated last month
- MAG Circularization Method☆33Updated 3 years ago
- Discover and annotate the virome☆42Updated last month
- ☆24Updated 6 years ago
- Strain Resolution ON Graphs☆47Updated last year
- Rapid and simple taxonomic profiling of genome and metagenome contigs☆28Updated last year
- 🍊 💫 Trim, circularise and orient long read bacterial genome assemblies☆26Updated 5 years ago
- Identify phage regions in bacterial genomes for masking purposes☆32Updated 5 years ago
- Strain Prediction and Analysis with Representative SEquence☆19Updated 5 months ago
- A k-mer based program for the identification of known plasmids from whole-genome sequencing reads☆35Updated 4 years ago
- Taxonomic classification of viruses at Order and Family level☆20Updated 2 years ago
- EzAAI - High Throughput Prokaryotic AAI Calculator☆41Updated 7 months ago
- MAGScoT - a MAG scoring and refinement tool☆35Updated 7 months ago
- Gene-flank analysis tool☆27Updated 5 months ago
- Get microbial sequence data easier and faster☆28Updated 5 years ago
- A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPs☆27Updated 7 months ago
- GTDB taxonomy taxdump files with trackable TaxIds☆53Updated last month
- Prophage Activity Estimator☆26Updated last year
- Inferring bacterial recombination rates from large-scale sequencing datasets.☆42Updated 2 years ago
- Phylogeny Enhanded Prediction of PAN-genome☆40Updated 4 years ago