karel-brinda / PhylignLinks
Alignment against all pre-2019 bacteria on laptops within a few hours (former MOF-Search)
β37Updated last year
Alternatives and similar repositories for Phylign
Users that are interested in Phylign are comparing it to the libraries listed below
Sorting:
- Phylogenetic compression of extremely large genome collections [661k βππ²ππΆπ | BIGSIdata βπ°π΄ππΆπ | AllTheBact'23 βπ³π±ππΆπ]β43Updated 6 months ago
- Strain-level haplotyping for metagenomes with short or long-reads.β55Updated 6 months ago
- Genome size estimation from long read overlapsβ61Updated 2 weeks ago
- Remove contaminated contigs from genomes using k-mers and taxonomies.β59Updated last year
- Recombination-free treesβ60Updated last month
- Python package to obtain, parse and explore biological taxonomies (GTDB, NCBI, Silva, Greengenes, OTT)β47Updated 3 months ago
- Automated strain separation of low-complexity metagenomesβ50Updated 3 years ago
- Fast and space-efficient taxonomic classification of long readsβ43Updated last month
- Mandrake πΏ/π¨βπ¬π¦ β Fast visualisation of the population structure of pathogens using Stochastic Cluster Embeddingβ38Updated 7 months ago
- Code to create a PRG from a Multiple Sequence Alignment fileβ25Updated last month
- PyO3 bindings and Python interface to skani, a method for fast genomic identity calculation using sparse chaining.β26Updated last month
- PanTax: Strain-level metagenomic profiling using pangenome graphsβ43Updated last month
- Simple-to-use interactive comparison of two bacterial genomesβ16Updated last month
- Python package to plot a phylogenetic tree on an existing matplotlib axis.β25Updated 2 months ago
- Colinear block visualisation toolβ31Updated last year
- SpydrPick: mutual information based detection of pairs of genomic loci co-evolving under a shared selective pressure.β13Updated 3 years ago
- Genomic neighbor typing of bacterial pathogens using MinHashβ43Updated 2 years ago
- A Python implementation of the OrthoANI algorithm for nucleotide identity measurement.β30Updated 2 months ago
- Microbial agile accurate SNP Typerβ29Updated last year
- Phylogenetic maximum representation sampling: choosing most representative strains or taxaβ39Updated 2 weeks ago
- software to identify primers that can distinguish genomesβ20Updated 8 months ago
- β17Updated last year
- Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomesβ15Updated 7 years ago
- GRIMER performs analysis of microbiome studies and generates a portable and interactive dashboard integrating annotation, taxonomy and meβ¦β22Updated 2 years ago
- PyO3 bindings and Python interface to sylph, an ultrafast method for containment ANI querying and taxonomic profiling.β20Updated 9 months ago
- β24Updated 8 months ago
- StrainXpress is a de novo assembly method which base on overlap-layout-consensus (OLC) paradigm and can fast and accurately assemble highβ¦β13Updated last year
- A mathematically characterized hypothesis test for organism presence/absence in a metagenomeβ32Updated last month
- Remove human reads from a sequencing runβ40Updated 2 months ago
- Plasmid analysis using rearrangement distancesβ45Updated last month