hallamlab / TreeSAPPLinks
A Python package for gene-centric taxonomic and functional classification using phylogenetic placement
☆25Updated last year
Alternatives and similar repositories for TreeSAPP
Users that are interested in TreeSAPP are comparing it to the libraries listed below
Sorting:
- A k-mer based program for the identification of known plasmids from whole-genome sequencing reads☆35Updated 4 years ago
- Ley Lab MetaGenome Profiler DataBase generator☆49Updated 2 years ago
- Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes☆54Updated 2 years ago
- Gene Absence Presence Identification tool.☆27Updated 6 months ago
- zol (& fai): large-scale targeted detection and evolutionary investigation of gene clusters (i.e. BGCs, phages, etc.)☆63Updated last week
- Bacterial GWAS analysis☆44Updated 2 months ago
- Identify phage regions in bacterial genomes for masking purposes☆34Updated 6 years ago
- Discover and annotate the virome☆53Updated last week
- A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPs☆31Updated 3 weeks ago
- Mapping-Assisted Targeted-Assembly for Metagenomics☆23Updated 6 months ago
- Predict plasmids from uncorrected long read data☆41Updated 5 years ago
- A toolkit for prokaryotic comparative genomics☆51Updated this week
- Phylogeny Enhanded Prediction of PAN-genome☆42Updated 5 years ago
- Remove contaminated contigs from genomes using k-mers and taxonomies.☆59Updated last year
- IslandPath standalone software☆33Updated last year
- EzAAI - High Throughput Prokaryotic AAI Calculator☆44Updated 2 months ago
- SCAPP is a plasmid assembly tool. This tool is described in our paper: https://microbiomejournal.biomedcentral.com/articles/10.1186/s4016…☆34Updated 2 years ago
- Calculate assocations between genes and traits☆28Updated 7 months ago
- ☆16Updated 5 years ago
- Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes☆35Updated 5 months ago
- Snakemake pipeline for downstream analysis of metagenome-assembled genomes (MAGs) (pronounced mag-pie)☆62Updated 2 years ago
- Bifrost graph gene caller.☆95Updated 3 weeks ago
- Predicting plasmid contigs from assemblies using single copy marker genes, plasmid genes, kmers - Developed by Linda van der Graaf☆49Updated last year
- Order and orientation of complete bacterial genomes☆28Updated 3 months ago
- MAGScoT - a MAG scoring and refinement tool☆37Updated last year
- post processing of bacterial pangenome gene presence/absence matrices☆61Updated 7 months ago
- TaxTriage is a Nextflow workflow designed to agnostically identify and classify microbial organisms within short- or long-read metagenomi…☆56Updated this week
- A tool for removing redundant genomes from a set of assemblies☆77Updated last month
- Gene-flank analysis tool☆32Updated 10 months ago
- BEAV: Bacterial Element Annotation reVamped☆70Updated last month