niemasd / TreeClusterLinks
Efficient phylogenetic clustering of viral sequences
☆90Updated 2 months ago
Alternatives and similar repositories for TreeCluster
Users that are interested in TreeCluster are comparing it to the libraries listed below
Sorting:
- CLI tool to annotate genes with KOfam☆88Updated 2 years ago
- Efficient phylogenetic tree inference for massive taxonomic datasets☆140Updated 9 months ago
- Python tool to reduce size and redundancy of phylogenetic datasets☆48Updated last month
- a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference☆81Updated 3 months ago
- FastOMA is a scalable software package to infer orthology relationship.☆86Updated this week
- SEER, reimplemented in python 🐍🔮☆128Updated 8 months ago
- Collection of scripts for bacterial genomics☆48Updated 6 years ago
- Amalgamated likelihood estimation (ALE) is a probabilistic approach to exhaustively explore all reconciled gene trees that can be amalgam…☆51Updated 8 months ago
- A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing☆68Updated 4 years ago
- PopPUNK 👨🎤 (POPulation Partitioning Using Nucleotide Kmers)☆103Updated 2 weeks ago
- An R package designed for drawing gene arrow maps☆95Updated 3 months ago
- Recentrifuge: robust comparative analysis and contamination removal for metagenomics☆99Updated 3 weeks ago
- A nextflow pipeline for decontamination of short reads, long reads and contigs☆55Updated 6 months ago
- Course materials for the Genomics Aotearoa Metagenomics Summer School, to be hosted at the University of Auckland in Septermber☆66Updated last year
- Detection of incorrectly labeled sequences across kingdoms☆88Updated 3 years ago
- A bioinformatic toolkit to align genome assemblies into pangenome graphs☆118Updated last week
- A Python package for obtaining complete lineages and the lowest common ancestor (LCA) from a set of taxonomic identifiers☆52Updated 2 months ago
- From genomes to phenotypes: Traitar, the microbial trait analyzer☆65Updated 6 years ago
- Split k-mer analysis – version 2☆103Updated 2 weeks ago
- A massively parallel tool for model selection and tree inference on thousands of genes☆51Updated last year
- ARG normalization by mapping to the ARO ontology.☆62Updated 5 months ago
- Precise host read removal☆114Updated 4 months ago
- Phylogenetic orthology inference for comparative genomics☆89Updated last week
- Follow up to Grace Blackwell's 661k dataset, for 2023☆128Updated 5 months ago
- PHANOTATE: a gene caller for phages.☆80Updated last year
- Best-fit model selection☆87Updated last year
- viralVerify: viral contig verification tool☆73Updated 4 years ago
- seqfu - Sequece Fastx Utilities☆124Updated last month
- Prediction of prophages from bacterial genomes☆81Updated 7 months ago
- ARTIC SARS-CoV-2 workflow and reporting☆50Updated 9 months ago