vinuesa / get_phylomarkersLinks
A pipeline to select optimal markers for microbial phylogenomics and species tree estimation using the multispecies coalescent and concatenation approaches
☆59Updated 2 weeks ago
Alternatives and similar repositories for get_phylomarkers
Users that are interested in get_phylomarkers are comparing it to the libraries listed below
Sorting:
- PATO is a R package designed to analyze pangenomes (set of genomes) intra or inter species.☆62Updated 2 years ago
- BEAV: Bacterial Element Annotation reVamped☆72Updated 4 months ago
- post processing of bacterial pangenome gene presence/absence matrices☆63Updated 9 months ago
- Using ggtree to build phylogenetic trees☆50Updated last year
- ☆54Updated 5 months ago
- A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPs☆32Updated 2 weeks ago
- EzAAI - High Throughput Prokaryotic AAI Calculator☆45Updated 4 months ago
- zol (& fai): large-scale targeted detection and evolutionary investigation of gene clusters (i.e. BGCs, phages, etc.)☆70Updated 3 weeks ago
- Snakemake pipeline for downstream analysis of metagenome-assembled genomes (MAGs) (pronounced mag-pie)☆62Updated 2 years ago
- Bioinformatics pipeline for recovery and analysis of metagenome-assembled genomes☆55Updated last month
- The Prokaryotic Genomics and Comparative Genomics Analysis Pipeline☆41Updated 3 years ago
- Gene Absence Presence Identification tool.☆27Updated 8 months ago
- MuDoGeR makes the recovery of genomes from prokaryotes, viruses, and eukaryotes from metagenomes easy.☆88Updated last year
- A tool for removing redundant genomes from a set of assemblies☆77Updated 3 months ago
- Bacterial GWAS analysis☆46Updated last month
- PlasmidID is a mapping-based, assembly-assisted plasmid identification tool that analyzes and gives graphic solution for plasmid identifi…☆41Updated 4 years ago
- A toolkit for prokaryotic comparative genomics☆51Updated 2 months ago
- ☆20Updated last year
- ☆24Updated 7 years ago
- Automatic eukaryotic taxonomic classification☆29Updated 7 months ago
- Calculate assocations between genes and traits☆29Updated 9 months ago
- SCAPP is a plasmid assembly tool. This tool is described in our paper: https://microbiomejournal.biomedcentral.com/articles/10.1186/s4016…☆35Updated 2 years ago
- Predicting plasmid contigs from assemblies using single copy marker genes, plasmid genes, kmers - Developed by Linda van der Graaf☆50Updated last year
- Bayesian inference of ancestral dates on bacterial phylogenetic trees☆93Updated last week
- An accurate and sensitive bacterial plasmid identification tool based on deep machine-learning of shared k-mers and genomic features.☆49Updated 2 years ago
- Python code for versatile Functional Ontology Assignments for Metagenomes searching via Hidden Markov Model (HMM) with environmental focu…☆63Updated last week
- a pipeline for reconciliation of phylogenetic histories within a bacterial pangenome☆50Updated 3 years ago
- A k-mer based program for the identification of known plasmids from whole-genome sequencing reads☆36Updated 4 years ago
- ☆33Updated 2 years ago
- IslandPath standalone software☆34Updated 2 years ago