Alignment-free Phylogenetic Placement using filtered SPAced word Matches
☆13Jul 19, 2023Updated 3 years ago
Alternatives and similar repositories for App-SpaM
Users that are interested in App-SpaM are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Phylogenetic Placement Evaluation Workflows : Benchmark placement software and different reference trees☆14Jan 31, 2025Updated last year
- Contains the code and workflow for the bacterial strain definition paper with Kostas Kostantinidis☆14Dec 4, 2023Updated 2 years ago
- ☆13Oct 2, 2026Updated 3 weeks ago
- R package for distilling functional annotations of bacterial genomes and metagenomes☆12Feb 27, 2025Updated last year
- CREST - Classification Resources for Environmnetal Sequence Tags, is a collection of software and databases for taxonomic classification …☆12Mar 20, 2022Updated 4 years ago
- Bare Metal GPUs on DigitalOcean Gradient AI • AdPurpose-built for serious AI teams training foundational models, running large-scale inference, and pushing the boundaries of what's possible.
- Automated processing of Sanger sequencing data, taxonomic profiling, and generation of microbial strain libraries☆19Jan 4, 2026Updated 9 months ago
- Sequential Tree Sampler for online phylogenetics☆16Mar 19, 2019Updated 7 years ago
- An HMM and Phylogenetic Placement based Ultra-Fast Taxonomy Assignment Tool for 16S sequencing☆11Oct 24, 2026Updated last week
- Protal is tool for taxonomic profiling from whole-genome shotgun sequencing data. With GTDB marker genes as reference, protal is able to …☆16Aug 10, 2026Updated 2 months ago
- Screening Historical Events of Recombination in a Phylogeny via Ancestral Sequences☆11Sep 3, 2025Updated last year
- microbial association network clustering algorithm☆14Dec 14, 2023Updated 2 years ago
- ☆23Mar 19, 2025Updated last year
- Calculate the normalizing factors for zeroinflated sequencing data such as microbiome sequencing data☆16Jan 31, 2025Updated last year
- ☆38Apr 13, 2026Updated 6 months ago
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- A graph-inspired data structure for determining likely chains of sequences from breadcrumbs of evidence☆17Jun 29, 2021Updated 5 years ago
- Tools for analyzing trees☆13Apr 16, 2025Updated last year
- A whole-genome reference database of soil bacteria, fungi, and archaea☆14Jun 19, 2026Updated 4 months ago
- A database for signatures of public genomic sources☆18Jul 18, 2026Updated 3 months ago
- Reference Phylogeny for Bacterial and Archaeal Genomes☆26Aug 9, 2025Updated last year
- Alignment-Based Sequence extraction☆15Feb 14, 2022Updated 4 years ago
- Predicting Absolute and Relative Abundance by Modeling Efficiency to Derive Intervals and Concentrations☆15Nov 24, 2025Updated 11 months ago
- WITCH is a multiple sequence alignment method that uses multiple weighted HMMs to align unaligned sequences and find consensuses.☆13Nov 18, 2025Updated 11 months ago
- Functions for phylogenetic analyses☆36May 18, 2026Updated 5 months ago
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- 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 7 years ago
- Inference of putative transmission phylogenetic clusters☆13Oct 13, 2020Updated 6 years ago
- MutTui pipeline to reconstruct mutational spectra for bacterial and viral datasets☆35Jul 27, 2026Updated 3 months ago
- FASSO: Functional Annotations using Sequence and Structure Orthology☆10Jan 17, 2023Updated 3 years ago
- rapidly rid reads of horrid humans☆15Dec 2, 2021Updated 4 years ago
- Biopsy - the Bioinformatic Optimisation System☆16Nov 1, 2015Updated 10 years ago
- A python tool for rapidly assessing the monophyly of user-defined groups in phylogenetic trees.☆12Apr 25, 2024Updated 2 years ago
- ☆12Sep 14, 2026Updated last month
- Semi-Automatic Taxonomy Improvement and Validation Algorithm☆21Jan 8, 2024Updated 2 years ago
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- Fungal Validation and Identification Pipeline☆16Oct 1, 2026Updated last month
- Fast implementation of the Neighbour-Joining method for phylogenetic inference☆21Sep 10, 2024Updated 2 years ago
- A set of scripts for calculating pairwise SNP distance☆45Feb 19, 2026Updated 8 months ago
- Tidy methods for Bayesian treatment effect models☆17Oct 23, 2026Updated last week
- Bacterial Operon Finder for Functional Organization☆16Nov 14, 2023Updated 2 years ago
- Fast and flexible tool for reading, modifying and writing biological sequences☆18Feb 4, 2026Updated 8 months ago
- For BRMS users who want to write models in Stan directly☆14May 14, 2025Updated last year