aaronmussig / PhyloDMLinks
Efficient calculation of phylogenetic distance matrices.
☆47Updated 11 months ago
Alternatives and similar repositories for PhyloDM
Users that are interested in PhyloDM are comparing it to the libraries listed below
Sorting:
- A Python implementation of the OrthoANI algorithm for nucleotide identity measurement.☆30Updated last month
- Phylogenetic maximum representation sampling: choosing most representative strains or taxa☆39Updated 5 months ago
- Strain-level haplotyping for metagenomes with short or long-reads.☆52Updated 5 months ago
- Python package to plot a phylogenetic tree on an existing matplotlib axis.☆24Updated last month
- Automated strain separation of low-complexity metagenomes☆50Updated 3 years ago
- More scalable dereplication for metagenome assembled genomes☆68Updated 3 weeks ago
- PyO3 bindings and Python interface to sylph, an ultrafast method for containment ANI querying and taxonomic profiling.☆20Updated 9 months ago
- Python package to obtain, parse and explore biological taxonomies (GTDB, NCBI, Silva, Greengenes, OTT)☆45Updated 2 months ago
- Phylogenetic compression of extremely large genome collections [661k ↘𝟭𝟲𝗚𝗶𝗕 | BIGSIdata ↘𝟰𝟴𝗚𝗶𝗕 | AllTheBact'23 ↘𝟳𝟱𝗚𝗶𝗕]☆41Updated 5 months ago
- alignment-free coverage calculation for metagenomic binning >100 times faster☆46Updated 6 months ago
- Remove contaminated contigs from genomes using k-mers and taxonomies.☆58Updated last year
- Genome size estimation from long read overlaps☆60Updated 2 weeks ago
- tree visualization for tree + annotation data☆40Updated 3 months ago
- Miscellaneous Perl scripts from 20 years in microbial bioinformatics☆17Updated last year
- Recombination-free trees☆60Updated 2 weeks ago
- Mandrake 🌿/👨🔬🦆 – Fast visualisation of the population structure of pathogens using Stochastic Cluster Embedding☆38Updated 6 months ago
- SHOOT.bio - the phylogenetic search engine☆25Updated 2 years ago
- FASTX search and [host] depletion using minimizers☆84Updated 2 weeks ago
- Remove human reads from a sequencing run☆39Updated last month
- Inferring bacterial recombination rates from large-scale sequencing datasets.☆42Updated 2 years ago
- Strain resolver for metagenomics☆78Updated last year
- Evaluating Nanopore-based bacterial variant calling☆19Updated last month
- skDER & CiDDER: efficient & high-resolution dereplication of microbial genomes.☆48Updated last week
- ☆17Updated last year
- Alignment against all pre-2019 bacteria on laptops within a few hours (former MOF-Search)☆37Updated last year
- Nail is an Alignment Inference tooL☆51Updated last week
- Microbial Genome Circular plotting tool for comparative genomics using Circos☆38Updated 2 years ago
- ☆51Updated 4 months ago
- Manipulate and generate figures for trees in Newick format☆22Updated last month
- PanTax: Strain-level metagenomic profiling using pangenome graphs☆42Updated 3 weeks ago