karel-brinda / PhylignLinks
Alignment against all pre-2019 bacteria on laptops within a few hours (former MOF-Search)
☆39Updated last year
Alternatives and similar repositories for Phylign
Users that are interested in Phylign are comparing it to the libraries listed below
Sorting:
- Strain-level haplotyping for metagenomes with short or long-reads.☆55Updated 6 months ago
- Genome size estimation from long read overlaps☆62Updated last month
- Phylogenetic compression of extremely large genome collections [661k ↘𝟭𝟲𝗚𝗶𝗕 | BIGSIdata ↘𝟰𝟴𝗚𝗶𝗕 | AllTheBact'23 ↘𝟳𝟱𝗚𝗶𝗕]☆43Updated 6 months ago
- Automated strain separation of low-complexity metagenomes☆51Updated 3 years ago
- Code to create a PRG from a Multiple Sequence Alignment file☆25Updated last month
- Fast and space-efficient taxonomic classification of long reads☆43Updated 2 months ago
- Genomic neighbor typing of bacterial pathogens using MinHash☆43Updated 2 years ago
- Mandrake 🌿/👨🔬🦆 – Fast visualisation of the population structure of pathogens using Stochastic Cluster Embedding☆38Updated 7 months ago
- Remove contaminated contigs from genomes using k-mers and taxonomies.☆59Updated last year
- PyO3 bindings and Python interface to skani, a method for fast genomic identity calculation using sparse chaining.☆27Updated 2 months ago
- Colinear block visualisation tool☆31Updated last year
- Recombination-free trees☆60Updated 2 months ago
- A new high-resolution long-read metagenome assembler for even noisy reads☆100Updated last month
- A mathematically characterized hypothesis test for organism presence/absence in a metagenome☆33Updated last month
- A Python implementation of the OrthoANI algorithm for nucleotide identity measurement.☆31Updated 3 months ago
- Plasmid analysis using rearrangement distances☆46Updated last month
- PanTax: Strain-level metagenomic profiling using pangenome graphs☆43Updated 2 months ago
- Better and faster Rust implementation of the FragGeneScan gene prediction model for short and error-prone reads.☆29Updated last month
- GRIMER performs analysis of microbiome studies and generates a portable and interactive dashboard integrating annotation, taxonomy and me…☆22Updated 2 years ago
- Microbial agile accurate SNP Typer☆29Updated last year
- ☆18Updated last year
- SpydrPick: mutual information based detection of pairs of genomic loci co-evolving under a shared selective pressure.☆13Updated 3 years ago
- Differential k-mer analysis☆37Updated last year
- Fast pairwise transmission inference from single genome and/or metagenomic data☆22Updated 3 months ago
- A methodology to rapidly leverage whole genome sequencing of bacterial isolates for clinical identification.☆34Updated 10 months ago
- ☆24Updated 9 months ago
- ☆30Updated 2 years ago
- Remove human reads from a sequencing run☆40Updated 3 months ago
- Simple-to-use interactive comparison of two bacterial genomes☆18Updated this week
- Python package to obtain, parse and explore biological taxonomies (GTDB, NCBI, Silva, Greengenes, OTT)☆47Updated 3 months ago