faylward / pangenomicsLinks
Scripts and utilities for pangenomic/phylogenomic analysis of prokaryotic genomes. Scripts for the analysis of genomic features such as C-ARSC, N-ARSC, and intergenic spacer lengths are also included.
☆10Updated 4 years ago
Alternatives and similar repositories for pangenomics
Users that are interested in pangenomics are comparing it to the libraries listed below
Sorting:
- A Swiss-Army-Knife for Bioinformaticians☆12Updated 3 weeks ago
- Find Prokaryotic DNA methylase genes in proteins, contigs, or genomes☆11Updated 11 months ago
- SynTracker is a pipeline, designated to determine the biological relatedness of conspecific strains (microbial strains of the same specie…☆31Updated 4 months ago
- ☆11Updated 2 years ago
- Rapid and simple taxonomic profiling of genome and metagenome contigs☆28Updated last year
- Draw pan- and core-genome curves from proteinortho output☆10Updated last year
- Set of utilities on sequences and BAM files☆27Updated 3 years ago
- ☆20Updated 3 years ago
- An R package to infer and analyze synteny networks from protein sequences☆30Updated 5 months ago
- Trans-Kingdom Marker Gene Pipeline for Taxonomic Profiling of Human Metagenomes☆19Updated last year
- Gene tree - species tree reconciliation from gene tree distributions☆29Updated this week
- Hierarchical clustering of cgMLST☆11Updated last year
- A simple-to-use tool for visualizing and comparing genome contexts for numerous genomes☆16Updated last year
- A Shiny app for taxonomic abundance visualization☆7Updated last year
- Pipeline for metagenome and metatranscriptome joint assembly☆21Updated 2 years ago
- ZGA prokaryotic genome assembly and annotation pipeline☆12Updated 8 months ago
- skDER & CiDDER: efficient & high-resolution dereplication of microbial genomes.☆45Updated 2 weeks ago
- Pathway Tools multiprocessing wrapper (for PathoLogic).☆14Updated 2 months ago
- Reproducible scripts and notebooks for 2019 paper on population genetics in metagenomes☆16Updated 5 years ago
- A tool to filter BUSCO output into single-copy gene files for phylogenomics☆13Updated 10 months ago
- Discover and annotate the virome☆42Updated last month
- Eukfinder: A pipeline to retrieve microbial eukaryote genomes from metagenomic sequencing data☆23Updated last month
- Prophage Tracer: precisely tracing prophages in prokaryotic genomes using overlapping split-read alignment☆24Updated 7 months ago
- Genomewide Epistasis Analysis on Bacteria☆14Updated 3 weeks ago
- Within-species genome-wide dN/dS estimation from very many genomes☆20Updated 4 years ago
- Repository for general metagenomics Nextflow pipeline☆16Updated this week
- http://huttenhower.sph.harvard.edu/waafle☆16Updated 5 months ago
- Small and simple scripts useful for various bioinformatics purposes e.g. extract sequences from fasta files☆20Updated 2 years ago
- ☆32Updated last year
- Fast and sensitive discovery of complete phages and prophages in bacterial genome sequences☆20Updated 5 months ago