Alternatives and similar repositories for ClonalFrameML

Users that are interested in ClonalFrameML are comparing it to the libraries listed below

• nigyta / dfast_core
  DDBJ Fast Annotation and Submission Tool
  ☆81Updated 3 months ago
• donovan-h-parks / CompareM
  A toolbox for comparative genomics.
  ☆104Updated 4 years ago
• SionBayliss / PIRATE
  A toolbox for pangenome analysis and threshold evaluation.
  ☆100Updated 3 years ago
• gbouras13 / hybracter
  Automated long-read first bacterial genome assembly tool implemented in Snakemake using Snaketool.
  ☆135Updated 2 months ago
• eead-csic-compbio / get_homologues
  GET_HOMOLOGUES: a versatile software package for pan-genome analysis
  ☆116Updated last month
• ncbi / fcs
  Foreign Contamination Screening caller scripts and documentation
  ☆133Updated 4 months ago
• HRGV / phyloFlash
  phyloFlash - A pipeline to rapidly reconstruct the SSU rRNAs and explore phylogenetic composition of an illumina (meta)genomic dataset.
  ☆87Updated last year
• fwhelan / coinfinder
  A tool for the identification of coincident (associating and dissociating) genes in pangenomes.
  ☆102Updated last year
• xavierdidelot / BactDating
  Bayesian inference of ancestral dates on bacterial phylogenetic trees
  ☆90Updated this week
• MDU-PHL / abritamr
  A pipeline for running AMRfinderPlus and collating results into functional classes
  ☆79Updated 11 months ago
• jhawkey / IS_mapper
  IS mapping software
  ☆56Updated 3 years ago
• bhattlab / MGEfinder
  A toolbox for identifying mobile genetic element (MGE) insertions from short-read sequencing data of bacterial isolates.
  ☆124Updated last year
• xiezhq / ISEScan
  A python pipeline to identify IS (Insertion Sequence) elements in genome and metagenome
  ☆96Updated 4 months ago
• qiyunlab / HGTector
  HGTector2: Genome-wide prediction of horizontal gene transfer based on distribution of sequence homology patterns.
  ☆136Updated last year
• patrickwest / EukRep
  Classification of Eukaryotic and Prokaryotic sequences from metagenomic datasets
  ☆73Updated last year
• marbl / parsnp
  Parsnp was designed to align the core genome of hundreds to thousands of bacterial genomes within a few minutes to few hours. Input can b…
  ☆145Updated 3 months ago
• ncbi / SKESA
  SKESA assembler
  ☆121Updated 9 months ago
• rrwick / Autocycler
  A tool for generating consensus long-read assemblies for bacterial genomes
  ☆160Updated this week
• avierstr / amplicon_sorter
  Sorts amplicons from Nanopore sequencing data based on similarity
  ☆38Updated 2 months ago
• lskatz / mashtree
  Create a tree using Mash distances
  ☆169Updated last year
• nmquijada / tormes
  Making whole bacterial genome sequencing data analysis easy
  ☆109Updated 3 months ago
• rrwick / Metagenomics-Index-Correction
  ☆83Updated last year
• songweizhi / MetaCHIP
  Horizontal gene transfer (HGT) identification pipeline
  ☆61Updated 2 years ago
• phac-nml / mob-suite
  MOB-suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies
  ☆153Updated 3 months ago
• aleimba / bac-genomics-scripts
  Collection of scripts for bacterial genomics
  ☆47Updated 5 years ago
• tseemann / snp-dists
  Pairwise SNP distance matrix from a FASTA sequence alignment
  ☆137Updated last year
• caitiecollins / treeWAS
  treeWAS: A Phylogenetic Tree-Based Tool for Genome-Wide Association Studies in Microbes
  ☆103Updated 6 months ago
• thanhleviet / ISfinder-sequences
  Insertion sequences (Insertion Element) [https://en.wikipedia.org/wiki/Insertion_sequence] collected from ISfinder (https://isfinder.biot…
  ☆68Updated 4 years ago
• gbouras13 / dnaapler
  Reorients assembled microbial sequences
  ☆124Updated 4 months ago
• B-UMMI / chewBBACA
  BSR-Based Allele Calling Algorithm
  ☆149Updated last week