JosephCrispell / homoplasyFinder
A tool to identify and annotate homoplasies on a phylogeny and sequence alignment
☆19Updated 3 years ago
Alternatives and similar repositories for homoplasyFinder:
Users that are interested in homoplasyFinder are comparing it to the libraries listed below
- ☆21Updated 10 years ago
- This repository provides source code for several pipelines dedicated to the alignment of nucleotide coding sequences that are based on MA…☆34Updated last year
- Recombination-free trees☆56Updated last year
- ☆36Updated 2 years ago
- Alignment-based retrieval and concatenation of phylogenetic markers from whole genome sequence (WGS) data☆35Updated 8 months ago
- reference-based long read assemblies of bacterial genomes☆47Updated 3 years ago
- A pipeline for performing genome-wide association tests for bacterial genomes.☆28Updated 6 years ago
- Long read metagenomics practical at EBAME18☆18Updated 6 years ago
- a pipeline for reconciliation of phylogenetic histories within a bacterial pangenome☆46Updated 2 years ago
- Alignment-Based Sequence extraction☆14Updated 2 years ago
- Automatic evaluation of HGTs☆26Updated 3 weeks ago
- PREQUAL: a pre-alignment quality filter for comparative sequence analyses☆31Updated 2 years ago
- Mobile Genetic Elements Retrieving Tool☆15Updated 3 years ago
- Predict plasmids from uncorrected long read data☆39Updated 5 years ago
- R package for comparison of synteny conservation at the genome-wide scale.☆14Updated 7 months ago
- Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes☆53Updated last year
- 🍊 💫 Trim, circularise and orient long read bacterial genome assemblies☆26Updated 5 years ago
- A genome-wide IM blockwise likelihood estimation toolkit☆15Updated 6 months ago
- ☆32Updated 4 years ago
- MCMCtreeR: A package to estimate distribution values for temporal node constraints and prepare input files for MCMCtree☆45Updated 5 years ago
- ☆38Updated last year
- Predict MLST directly from uncorrected long reads☆26Updated 2 years ago
- STAG: Species Tree from All Genes☆32Updated 6 years ago
- A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPs☆25Updated 2 months ago
- Miscellaneous Perl scripts from 20 years in microbial bioinformatics☆17Updated 6 months ago
- Toolkit for preparing genomes for submission to NCBI☆29Updated 3 years ago
- post processing of bacterial pangenome gene presence/absence matrices☆54Updated 4 months ago
- Workflow for detecting genome-wide horizontal gene transfers☆10Updated 6 years ago
- a tool to filter sites in a FASTA-format whole-genome pseudo-alignment☆41Updated last month
- A massively parallel tool for model selection and tree inference on thousands of genes☆46Updated 10 months ago