Alignment-free Phylogenetic Placement using filtered SPAced word Matches
☆12Jul 19, 2023Updated 2 years ago
Alternatives and similar repositories for App-SpaM
Users that are interested in App-SpaM are comparing it to the libraries listed below
Sorting:
- Phylogenetic Placement Evaluation Workflows : Benchmark placement software and different reference trees☆12Jan 31, 2025Updated last year
- CREST - Classification Resources for Environmnetal Sequence Tags, is a collection of software and databases for taxonomic classification …☆12Mar 20, 2022Updated 3 years ago
- A database for signatures of public genomic sources☆18Jan 1, 2026Updated 2 months ago
- microbial association network clustering algorithm☆14Dec 14, 2023Updated 2 years ago
- rapidly rid reads of horrid humans☆15Dec 2, 2021Updated 4 years ago
- A graph-inspired data structure for determining likely chains of sequences from breadcrumbs of evidence☆17Jun 29, 2021Updated 4 years ago
- Calculate the normalizing factors for zeroinflated sequencing data such as microbiome sequencing data☆16Jan 31, 2025Updated last year
- Fast implementation of the Neighbour-Joining method for phylogenetic inference☆18Sep 10, 2024Updated last year
- Sequential Tree Sampler for online phylogenetics☆16Mar 19, 2019Updated 6 years ago
- ☆21Mar 19, 2025Updated 11 months ago
- Streaming assembly for MinION data☆25Dec 16, 2023Updated 2 years ago
- distance based phylogenetic placement☆27Feb 28, 2024Updated 2 years ago
- Functions for phylogenetic analyses☆36Nov 10, 2025Updated 3 months ago
- An algorithm for recovering haplotypes from metagenomes☆30Jun 29, 2021Updated 4 years ago
- Iterate over minimizers of a DNA sequence☆31Jul 12, 2024Updated last year
- Estimating k-mer coverage histogram of genomics data☆77Dec 13, 2023Updated 2 years ago
- A tool to extract and annotate genes from raw RNA-seq reads.☆10Dec 20, 2024Updated last year
- annotating microbial co-occurrence networks☆12Oct 7, 2025Updated 4 months ago
- GPRuler, an open-source computational framework to automate the reconstruction process of Gene-Protein-Reaction (GPR) rules within metabo…☆11Oct 11, 2022Updated 3 years ago
- ☆38Apr 8, 2022Updated 3 years ago
- Detects and blacklists paralog RAD loci analyzed in Stacks or ipyrad, based on the McKinney 2017 method (doi:10.1111/1755-0998.12613)☆10Sep 4, 2019Updated 6 years ago
- ☆11Apr 5, 2021Updated 4 years ago
- ☆14Jul 4, 2015Updated 10 years ago
- community detection in multiplex networks☆10Apr 23, 2016Updated 9 years ago
- ☆11Feb 16, 2021Updated 5 years ago
- Scotch pipeline for indel calling.☆10Nov 25, 2019Updated 6 years ago
- ntHash implementation in Rust☆36Jul 12, 2024Updated last year
- A web application framework for analysis and visualization of High throughput Sequencing metagenomic data☆10Nov 21, 2016Updated 9 years ago
- ☆10Mar 24, 2025Updated 11 months ago
- Uncover organisms' metabolic blueprints☆13Jun 18, 2024Updated last year
- A python tool for rapidly assessing the monophyly of user-defined groups in phylogenetic trees.☆10Apr 25, 2024Updated last year
- Command line client and Python libraries for CosmosID API☆12Oct 28, 2025Updated 4 months ago
- ☆13Aug 13, 2024Updated last year
- Metagenomic Intra-Species Diversity Analysis (MIDAS)☆42Sep 3, 2024Updated last year
- Kmer-db is a fast and memory-efficient tool for large-scale k-mer analyses (indexing, querying, estimating evolutionary relationships, et…☆97May 20, 2025Updated 9 months ago
- Feature Aggregate Depth Utility☆12Aug 20, 2024Updated last year
- Fast and compact locality-preserving minimal perfect hashing for k-mer sets.☆43Nov 18, 2023Updated 2 years ago
- ☆10Aug 21, 2025Updated 6 months ago
- Wrapper over rust-htslib for building collections of BAM records for testing.☆10Dec 1, 2025Updated 3 months ago