NicolaDM / phastSimLinks
fast sequence evolution simulation for SARS-CoV-2 and similar
☆22Updated 5 months ago
Alternatives and similar repositories for phastSim
Users that are interested in phastSim are comparing it to the libraries listed below
Sorting:
- Alignment against all pre-2019 bacteria on laptops within a few hours (former MOF-Search)☆37Updated last year
- Phylogenetic compression of extremely large genome collections [661k ↘𝟭𝟲𝗚𝗶𝗕 | BIGSIdata ↘𝟰𝟴𝗚𝗶𝗕 | AllTheBact'23 ↘𝟳𝟱𝗚𝗶𝗕]☆41Updated 5 months ago
- distance based phylogenetic placement☆26Updated last year
- Python bindings for the TaxonKit library☆40Updated 2 months ago
- Python package to obtain, parse and explore biological taxonomies (GTDB, NCBI, Silva, Greengenes, OTT)☆45Updated 2 months ago
- Python package to plot a phylogenetic tree on an existing matplotlib axis.☆24Updated 2 months ago
- Remove contaminated contigs from genomes using k-mers and taxonomies.☆59Updated last year
- Efficient calculation of phylogenetic distance matrices.☆47Updated 11 months ago
- Cython bindings and Python interface to FastANI, a method for fast whole-genome similarity estimation.☆22Updated 2 weeks ago
- ☆17Updated 3 years ago
- Design degenerated primers on highly variable alignments for full genome sequencing or qPCR. Specifically developed for viruses.☆41Updated last month
- Automated strain separation of low-complexity metagenomes☆50Updated 3 years ago
- Better and faster Rust implementation of the FragGeneScan gene prediction model for short and error-prone reads.☆26Updated last month
- Fast and space-efficient taxonomic classification of long reads☆43Updated 3 weeks ago
- A Pyrodigal extension to predict genes in giant viruses and viruses with alternative genetic code.☆18Updated last month
- Rapid discovery of novel prophages using biological feature engineering and machine learning☆36Updated 9 months ago
- Fast implementation of KofamScan optimized for high-memory systems using PyHMMER☆14Updated 2 weeks ago
- Bacterial Annotation by Learned Representation of Genes☆58Updated 4 years ago
- PyO3 bindings and Python interface to skani, a method for fast genomic identity calculation using sparse chaining.☆26Updated last month
- Strain-level haplotyping for metagenomes with short or long-reads.☆52Updated 5 months ago
- 🚦🧬 Binning Metagenomic Contigs via Composition, Coverage and Assembly Graphs☆65Updated 11 months ago
- PyO3 bindings and Python interface to sylph, an ultrafast method for containment ANI querying and taxonomic profiling.☆20Updated 9 months ago
- alignment-free coverage calculation for metagenomic binning >100 times faster☆46Updated 6 months ago
- Phylogenetic maximum representation sampling: choosing most representative strains or taxa☆39Updated 5 months ago
- A Python package for obtaining complete lineages and the lowest common ancestor (LCA) from a set of taxonomic identifiers☆50Updated 7 months ago
- A workflow and scripts for large-scale antiSMASH analyses☆42Updated 5 months ago
- RabbitTClust: enabling fast clustering analysis of millions bacteria genomes with MinHash sketches☆49Updated last month
- Universal and efficient structure-based core gene phylogeny with Foldseek and ProstT5☆75Updated 3 months ago
- SHOOT.bio - the phylogenetic search engine☆25Updated 2 years ago
- A pipeline for high-quality bacterial genome construction using ONT sequencing☆39Updated 3 years ago