A Python package for gene-centric taxonomic and functional classification using phylogenetic placement
☆26Sep 3, 2024Updated last year
Alternatives and similar repositories for TreeSAPP
Users that are interested in TreeSAPP are comparing it to the libraries listed below
Sorting:
- Protocols, data and code associated with the MK-SpikeSeq method for quantifying the absolute abundances of microbiota samples☆12May 19, 2021Updated 4 years ago
- Easy-to-use web application for visualization and comparison of genomes in Genbank file☆22May 27, 2022Updated 3 years ago
- Python package for common tasks in bioinformatic.☆12Sep 24, 2025Updated 5 months ago
- frame-shift correction for long-read (meta)genomics☆33Dec 11, 2023Updated 2 years ago
- StrainXpress is a de novo assembly method which base on overlap-layout-consensus (OLC) paradigm and can fast and accurately assemble high…☆13Mar 7, 2024Updated 2 years ago
- 🦠🧬🧑💻📇 Microbial genomes-to-report pipeline☆74Mar 14, 2026Updated last week
- GraftM - Rapid community profiles from metagenomes☆50Nov 6, 2025Updated 4 months ago
- ☆50Jan 4, 2026Updated 2 months ago
- Repository of the integrated mouse gut metagenomic catalog☆20Mar 14, 2022Updated 4 years ago
- Plot genome alignment figure using progressiveMauve & genoPlotR☆22Aug 5, 2022Updated 3 years ago
- Plot multiple sequence alignment (MSA)☆16Sep 23, 2024Updated last year
- highthroughput rRNA sequence classification and OTU mapping for metagenomic samples☆25Nov 3, 2023Updated 2 years ago
- Graph Splitting Method☆13Jul 10, 2019Updated 6 years ago
- Tool for constructing phylogenies and summarizing metabolic characteristics based on curated and custom profile HMMs☆17Feb 5, 2022Updated 4 years ago
- phyloFlash - A pipeline to rapidly reconstruct the SSU rRNAs and explore phylogenetic composition of an illumina (meta)genomic dataset.☆89Oct 27, 2023Updated 2 years ago
- 🧬 MSABrowser: dynamic and fast visualization of sequence alignments, variations, and annotations☆37May 21, 2024Updated last year
- hAMRoaster is an analysis pipeline that can compare the output of tools for detecting AMR genes and provide metrics of their performance☆22Mar 8, 2024Updated 2 years ago
- ViromeScan allows the user to explore and taxonomically characterize the virome from metagenomic reads, efficiently denoising samples fro…☆13Feb 13, 2023Updated 3 years ago
- MetaCarvel: A scaffolder for metagenomes☆14Sep 17, 2024Updated last year
- ⚡️🧬 FastMLST: A multi-core tool for multilocus sequence typing of draft genome assemblies☆25Nov 19, 2025Updated 4 months ago
- A whole-genome and alignment-free prokaryotic phylogeny tool☆23Mar 9, 2025Updated last year
- Assort phage protein sequences into phamilies using MMseqs2☆12Dec 16, 2024Updated last year
- 🦠🧬 Unraveling Viral Genomes from Metagenomes☆10Oct 3, 2025Updated 5 months ago
- An ATAC-seq pipeline wrapped in NextFlow that can be run by Jupyter☆14Jan 18, 2019Updated 7 years ago
- [Archived] SnakeMake pipeline to run BlobTools on public assemblies☆11Jul 3, 2023Updated 2 years ago
- UFCG: Universal Fungal Core Genes☆36Jul 29, 2025Updated 7 months ago
- CLI to automate Nextflow pipeline testing☆12Dec 15, 2025Updated 3 months ago
- From genomes to phenotypes: Traitar3, the microbial trait analyzer (for Python3)☆21Jul 8, 2024Updated last year
- Finding prophage regions in bacterial genomes using brute force☆22Jan 20, 2023Updated 3 years ago
- Close assembly gaps using long-reads at high accuracy.☆51Feb 20, 2024Updated 2 years ago
- A tool for classifying prokaryote protein sequences into COG(Cluster of Orthologous Genes) functional category☆82May 3, 2025Updated 10 months ago
- Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes☆35Apr 26, 2025Updated 10 months ago
- Unsupervised Clustering of Environmental Microbial Assemblies Using Coverage and Affinity Propagation☆31May 25, 2021Updated 4 years ago
- Generic but comprehensive pipeline for prokaryotic genome annotation and interrogation with interactive reports and shiny app.☆106Jan 22, 2026Updated last month
- Inference of putative transmission phylogenetic clusters☆12Oct 13, 2020Updated 5 years ago
- finding conserved regions in highly diverse genomes☆16Jun 1, 2025Updated 9 months ago
- 🧬 Efficient parallelized peta-scale protein database search☆40Jan 4, 2024Updated 2 years ago
- WITCH is a multiple sequence alignment method that uses multiple weighted HMMs to align unaligned sequences and find consensuses.☆13Nov 18, 2025Updated 4 months ago
- Alignment-free Phylogenetic Placement using filtered SPAced word Matches☆12Jul 19, 2023Updated 2 years ago