Alternatives and similar repositories for StrainFacts

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

• santeripuranen / SpydrPick
  SpydrPick: mutual information based detection of pairs of genomic loci co-evolving under a shared selective pressure.
  ☆13Updated 3 years ago
• weisberglab / beav
  BEAV: Bacterial Element Annotation reVamped
  ☆70Updated 2 months ago
• gtonkinhill / fastbaps
  A fast approximation to a Dirichlet Process Mixture model (DPM) for clustering genetic data
  ☆66Updated 3 years ago
• kussell-lab / mcorr
  Inferring bacterial recombination rates from large-scale sequencing datasets.
  ☆42Updated 2 years ago
• microbial-pangenomes-lab / microGWAS
  Bacterial GWAS analysis
  ☆45Updated 3 months ago
• WatsonLab / MAGpy
  Snakemake pipeline for downstream analysis of metagenome-assembled genomes (MAGs) (pronounced mag-pie)
  ☆62Updated 2 years ago
• christophertbrown / iRep
  scripts for estimating bacteria replication rates based on population genome copy number variation
  ☆72Updated 5 years ago
• flass / pantagruel
  a pipeline for reconciliation of phylogenetic histories within a bacterial pangenome
  ☆50Updated 3 years ago
• leylabmpi / Struo
  Ley Lab MetaGenome Profiler DataBase generator
  ☆49Updated 2 years ago
• rrwick / Verticall
  Recombination-free trees
  ☆60Updated last month
• hoelzer-lab / ribap
  A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPs
  ☆31Updated 3 weeks ago
• leylabmpi / SynTracker
  SynTracker is a pipeline, designated to determine the biological relatedness of conspecific strains (microbial strains of the same specie…
  ☆35Updated last month
• brinkmanlab / islandpath
  IslandPath standalone software
  ☆33Updated last year
• wtmatlock / flanker
  Gene-flank analysis tool
  ☆33Updated 10 months ago
• zheminzhou / PEPPAN
  Phylogeny Enhanded Prediction of PAN-genome
  ☆42Updated 5 years ago
• ChrispinChaguza / RCandy
  RCandy: an R package for visualising homologous recombination events in bacterial genomes
  ☆25Updated 3 years ago
• irycisBioinfo / PATO
  PATO is a R package designed to analyze pangenomes (set of genomes) intra or inter species.
  ☆62Updated 2 years ago
• santirdnd / COPLA
  A taxonomic classifier of plasmids
  ☆28Updated 4 years ago
• AlexanderLabWHOI / EUKulele
  Automatic eukaryotic taxonomic classification
  ☆28Updated 5 months ago
• ikmb / MAGScoT
  MAGScoT - a MAG scoring and refinement tool
  ☆37Updated last year
• mw55309 / ideel
  Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes
  ☆54Updated 2 years ago
• snayfach / MAGpurify
  Improvement of metagenome-assembled genomes
  ☆54Updated 5 years ago
• valflanza / accnet
  ☆13Updated 8 years ago
• bluenote-1577 / fairy
  alignment-free coverage calculation for metagenomic binning >100 times faster
  ☆48Updated 7 months ago
• MrTomRod / scoary-2
  Calculate assocations between genes and traits
  ☆28Updated 7 months ago
• simonrharris / SKA
  Split Kmer Analysis
  ☆65Updated 3 years ago
• quadram-institute-bioscience / socru
  Order and orientation of complete bacterial genomes
  ☆28Updated 3 months ago
• mtisza1 / Cenote-Taker3
  Discover and annotate the virome
  ☆53Updated last week
• SWittouck / SCARAP
  A toolkit for prokaryotic comparative genomics
  ☆51Updated last week
• dib-lab / charcoal
  Remove contaminated contigs from genomes using k-mers and taxonomies.
  ☆59Updated last year