lczech / gappaLinks
A toolkit for analyzing and visualizing phylogenetic placement data
☆63Updated last month
Alternatives and similar repositories for gappa
Users that are interested in gappa are comparing it to the libraries listed below
Sorting:
- Simka and SimkaMin are comparative metagenomics methods dedicated to NGS datasets.☆50Updated 3 years ago
- Massively parallel phylogenetic placement of genetic sequences☆86Updated 3 years ago
- SHallow shOtGUN profiler☆53Updated 3 years ago
- A nextflow pipeline for decontamination of short reads, long reads and contigs☆55Updated 4 months ago
- Inferring bacterial recombination rates from large-scale sequencing datasets.☆42Updated 2 years ago
- A fast approximation to a Dirichlet Process Mixture model (DPM) for clustering genetic data☆68Updated 3 years ago
- a pipeline for reconciliation of phylogenetic histories within a bacterial pangenome☆50Updated 3 years ago
- BEAV: Bacterial Element Annotation reVamped☆72Updated 2 months ago
- Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes☆54Updated 2 years ago
- Gene-flank analysis tool☆33Updated 11 months ago
- Visualize whole genome alignments as linear maps☆73Updated 3 months ago
- Snakemake pipeline for downstream analysis of metagenome-assembled genomes (MAGs) (pronounced mag-pie)☆62Updated 2 years ago
- starfish: a modular toolkit for giant mobile element annotation☆33Updated 11 months ago
- De novo Extraction of Strains from MetAgeNomes☆71Updated 5 years ago
- Please use mmgenome2 instead. Tools for extracting individual genomes from metagenomes☆27Updated 8 years ago
- Phylogenetic and taxonomic analysis for genomes and metagenomes☆82Updated 9 years ago
- Parse NCBI taxonomy and accessions to find taxonomic assignments☆77Updated 3 months ago
- StaG Metagenomic Workflow Collaboration☆28Updated last year
- Fast k-mer based tool for multi locus sequence typing (MLST)☆45Updated 5 years ago
- MicrobeCensus estimates the average genome size of microbial communities from metagenomic data☆45Updated 5 years ago
- Fast and pretty dotplots for whole genomes assemblies using minimap and R/ggplot2☆76Updated 9 years ago
- Phylogenetics between and within hosts at once, all along the genome.☆50Updated last year
- This is the codebase for Recycler, described in our manuscript: https://academic.oup.com/bioinformatics/article/33/4/475/2623362, by Roye…☆58Updated 4 years ago
- Genome wide orthology inference and dNdS estimation☆96Updated 2 months ago
- Recombination-free trees☆60Updated 2 months ago
- GATB Minia assembly pipeline☆31Updated 2 years ago
- Bifrost graph gene caller.☆95Updated last month
- FlexTaxD (Flexible Taxonomy Databases) - Create, add, merge different taxonomy sources (QIIME, GTDB, NCBI and more) and create metagenomi…☆67Updated 8 months ago
- AMPtk: Amplicon ToolKit for NGS data (formally UFITS)☆39Updated 2 years ago
- Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWoo…☆56Updated 3 years ago