balabanmetin / applesLinks
distance based phylogenetic placement
☆27Updated last year
Alternatives and similar repositories for apples
Users that are interested in apples are comparing it to the libraries listed below
Sorting:
- Alignment against all pre-2019 bacteria on laptops within a few hours (former MOF-Search)☆39Updated last year
- Phylogenetic maximum representation sampling: choosing most representative strains or taxa☆40Updated 2 months ago
- Efficient calculation of phylogenetic distance matrices.☆49Updated last year
- Automated strain separation of low-complexity metagenomes☆53Updated 4 years ago
- Mandrake 🌿/👨🔬🦆 – Fast visualisation of the population structure of pathogens using Stochastic Cluster Embedding☆39Updated 9 months ago
- PREQUAL: a pre-alignment quality filter for comparative sequence analyses☆33Updated 3 years ago
- Non-redundant pangenome assemblies from multiple genomes or bins☆14Updated 7 months ago
- Remove contaminated contigs from genomes using k-mers and taxonomies.☆59Updated 2 years ago
- PyO3 bindings and Python interface to sylph, an ultrafast method for containment ANI querying and taxonomic profiling.☆20Updated last year
- Fast and space-efficient taxonomic classification of long reads☆43Updated 3 months ago
- Remove human reads from a sequencing run☆46Updated this week
- Strain-level haplotyping for metagenomes with short or long-reads.☆59Updated 8 months ago
- Python package to plot a phylogenetic tree on an existing matplotlib axis.☆26Updated 4 months ago
- Recombination-free trees☆62Updated 3 months ago
- Phylogenetic compression of extremely large genome collections [661k ↘𝟭𝟲𝗚𝗶𝗕 | BIGSIdata ↘𝟰𝟴 𝗚𝗶𝗕 | AllTheBact'23 ↘𝟳𝟱𝗚𝗶𝗕]☆43Updated 8 months ago
- Genomic neighbor typing of bacterial pathogens using MinHash☆43Updated 2 years ago
- ☆43Updated last year
- A Python implementation of the OrthoANI algorithm for nucleotide identity measurement.☆31Updated 4 months ago
- ⚡️ 🧬 Fulgor is a fast and space-efficient colored de Bruijn graph index.☆57Updated 3 weeks ago
- PanTax: Strain-level metagenomic profiling using pangenome graphs☆45Updated 3 months ago
- Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database☆42Updated 5 years ago
- Get microbial sequence data easier and faster☆28Updated 6 years ago
- Gene-flank analysis tool☆34Updated last year
- HyGen: Compact and Efficient Genome Sketching using Hyperdimensional Vectors☆30Updated last year
- Nail is an Alignment Inference tooL☆54Updated last week
- Fast and accurate tool for estimating genomic distances between genome-skims☆47Updated 2 years ago
- Evaluating Nanopore-based bacterial variant calling☆21Updated 4 months ago
- A new high-resolution long-read metagenome assembler for even noisy reads☆109Updated 3 months ago
- Manipulate and generate figures for trees in Newick format☆22Updated 4 months ago
- Python package to obtain, parse and explore biological taxonomies (GTDB, NCBI, Silva, Greengenes, OTT)☆47Updated 5 months ago