somme89 / rapidNJ
Fast implementation of the Neighbour-Joining method for phylogenetic inference
☆15Updated 5 months ago
Alternatives and similar repositories for rapidNJ:
Users that are interested in rapidNJ are comparing it to the libraries listed below
- Genome size estimation from long read overlaps☆48Updated 2 months ago
- Strain-level haplotyping for metagenomes with short or long-reads.☆50Updated 7 months ago
- Plasmid analysis using rearrangement distances☆31Updated 3 months ago
- Intra-species bacterial contamination detection☆25Updated last week
- Variant call verification☆16Updated last month
- Remove human reads from a sequencing run☆36Updated 4 months ago
- Standalone Python re-implementation of the POLCA polisher from MaSuRCA☆30Updated 5 months ago
- Colinear block visualisation tool☆30Updated last year
- SpydrPick: mutual information based detection of pairs of genomic loci co-evolving under a shared selective pressure.☆13Updated 2 years ago
- PyO3 bindings and Python interface to skani, a method for fast genomic identity calculation using sparse chaining.☆27Updated this week
- Fast and scalable nanopore adaptive sampling☆33Updated last year
- Software that separates very close sequences that have been collapsed during assembly. Uses only long reads.☆34Updated 2 months ago
- Rapid and simple taxonomic profiling of genome and metagenome contigs☆27Updated last year
- Haplotype-aware genome assembly toolkit☆29Updated 5 years ago
- Phylogenetic maximum representation sampling: choosing most representative strains or taxa☆36Updated 2 months ago
- 🍊 💫 Trim, circularise and orient long read bacterial genome assemblies☆26Updated 5 years ago
- CFSAN Shigella Typing Pipeline☆14Updated last year
- Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes☆15Updated 6 years ago
- Comparison pipeline for Prokaryote Protein Coding Gene Predictors☆22Updated 10 months ago
- Code to create a PRG from a Multiple Sequence Alignment file☆23Updated 10 months ago
- Pangenome Sequence Naming: a backwards-compatible hack to simplify the identification of samples and haplotypes in pangenomes☆38Updated 4 months ago
- Get microbial sequence data easier and faster☆28Updated 5 years ago
- Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)☆24Updated 4 months ago
- Fast long-read mapper and whole-genome aligner (accelerated version of minimap2)☆27Updated last month
- A Python implementation of the OrthoANI algorithm for nucleotide identity measurement.☆22Updated this week
- skDER & CiDDER: efficient & high-resolution dereplication of microbial genomes to select representatives for comparative genomics and met…☆43Updated this week
- Python package to plot a phylogenetic tree on an existing matplotlib axis.☆15Updated last month
- Population analysis PIPEline 🛠🧬☆16Updated this week
- Microbial agile accurate SNP Typer☆29Updated last year
- Differential k-mer analysis☆34Updated last year