Alternatives and similar repositories for Phylowave_Learning-fitness-dynamics-pathogens-in-phylogenies

Users that are interested in Phylowave_Learning-fitness-dynamics-pathogens-in-phylogenies are comparing it to the libraries listed below

• AMRverse / AMRrules
  Interpretative standards for AMR genotypes
  ☆25Updated last week
• clockor2 / clockor2
  Inferring global and local strict molecular clocks using root-to-tip regression
  ☆13Updated 5 months ago
• broadinstitute / delphy
  Fast, scalable, accurate and accessible Bayesian phylogenetics
  ☆40Updated 3 weeks ago
• flass / pantagruel
  a pipeline for reconciliation of phylogenetic histories within a bacterial pangenome
  ☆50Updated 3 years ago
• JosephCrispell / homoplasyFinder
  A tool to identify and annotate homoplasies on a phylogeny and sequence alignment
  ☆20Updated 4 years ago
• weisberglab / beav
  BEAV: Bacterial Element Annotation reVamped
  ☆72Updated 2 months ago
• tgvaughan / bacter
  Bacterial phylogenetics in BEAST 2.
  ☆18Updated 2 years ago
• larssnip / micropan
  R package for microbial pangenomics
  ☆24Updated 3 years ago
• MrTomRod / scoary-2
  Calculate assocations between genes and traits
  ☆28Updated 7 months ago
• rrwick / Verticall
  Recombination-free trees
  ☆60Updated 2 months ago
• gtonkinhill / fastbaps
  A fast approximation to a Dirichlet Process Mixture model (DPM) for clustering genetic data
  ☆67Updated 3 years ago
• tseemann / cgmlst-dists
  🐻⇔🐨 Calculate distance matrix from ChewBBACA cgMLST allele call tables
  ☆29Updated 2 years ago
• richardmleggett / MARTi
  Metagenomic Analysis in Real Time
  ☆28Updated last week
• santeripuranen / SpydrPick
  SpydrPick: mutual information based detection of pairs of genomic loci co-evolving under a shared selective pressure.
  ☆13Updated 3 years ago
• metagenopolis / CroCoDeEL
  CroCoDeEL is a tool that detects cross-sample contamination in shotgun metagenomic data
  ☆24Updated 2 months ago
• xavierdidelot / TransPhylo
  Reconstruction of transmission trees using genomic data
  ☆63Updated 2 years ago
• kussell-lab / mcorr
  Inferring bacterial recombination rates from large-scale sequencing datasets.
  ☆42Updated 2 years ago
• wtmatlock / flanker
  Gene-flank analysis tool
  ☆33Updated 10 months ago
• Arcadia-Science / sourmashconsumr
  Working with the outputs of sourmash in R
  ☆27Updated last year
• mtisza1 / Cenote-Taker3
  Discover and annotate the virome
  ☆53Updated 2 weeks ago
• aweimann / traitar
  ☆22Updated 2 years ago
• MDU-PHL / bohra
  A pipeline for bioinformatics analysis of bacterial genomes
  ☆30Updated last week
• flu-crew / parnas
  Phylogenetic maximum representation sampling: choosing most representative strains or taxa
  ☆40Updated last month
• klebgenomics / Kaptive
  ☆55Updated this week
• soedinglab / transannot
  TransAnnot - a fast transcriptome annotation pipeline
  ☆19Updated 9 months ago
• bacpop / CELEBRIMBOR
  Core ELEment Bias Removal In Metagenome Binned ORthologs: A pipeline to make pangenomes from MAGs
  ☆25Updated last year
• BDI-pathogens / phyloscanner
  Phylogenetics between and within hosts at once, all along the genome.
  ☆50Updated last year
• WatsonLab / MAGpy
  Snakemake pipeline for downstream analysis of metagenome-assembled genomes (MAGs) (pronounced mag-pie)
  ☆62Updated 2 years ago
• leaemiliepradier / PlasForest
  A random forest classifier to identify contigs of plasmid origin in contig and scaffold genomes
  ☆19Updated 2 years ago
• ChrispinChaguza / RCandy
  RCandy: an R package for visualising homologous recombination events in bacterial genomes
  ☆25Updated 3 years ago