Alternatives and similar repositories for GenoFLU

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

• flu-crew / TreeSort
  Virus reassortment inference software. Infers both recent and ancestral reassortment and uses flexible molecular clock constraints.
  ☆13Updated last month
• flu-crew / parnas
  Phylogenetic maximum representation sampling: choosing most representative strains or taxa
  ☆38Updated last month
• sdellicour / seraphim
  R package for studying environmental rasters and phylogenetic informed movements (Dellicour et al. 2016, Bioinformatics; Dellicour et al.…
  ☆34Updated last month
• tseemann / cgmlst-dists
  🐻⇔🐨 Calculate distance matrix from ChewBBACA cgMLST allele call tables
  ☆27Updated last year
• flass / pantagruel
  a pipeline for reconciliation of phylogenetic histories within a bacterial pangenome
  ☆48Updated 2 years ago
• weisberglab / beav
  BEAV: Bacterial Element Annotation reVamped
  ☆65Updated 6 months ago
• pollardlab / MIDAS
  Metagenomic Intra-Species Diversity Analysis (MIDAS)
  ☆37Updated 8 months ago
• gtonkinhill / fastbaps
  A fast approximation to a Dirichlet Process Mixture model (DPM) for clustering genetic data
  ☆62Updated 2 years ago
• DOH-JDJ0303 / bigbacter-nf
  Bacterial surveillance pipeline.
  ☆24Updated this week
• asmngs / asmngs20
  ASMNGS20 - 2020 Conference Details
  ☆15Updated 2 years ago
• rrwick / Verticall
  Recombination-free trees
  ☆58Updated last month
• richardmleggett / MARTi
  Metagenomic Analysis in Real Time
  ☆24Updated last month
• boulund / phaster_scripts
  Small utility script to submit genomes to PHASTER for phage detection
  ☆24Updated 3 years ago
• metagenopolis / CroCoDeEL
  CroCoDeEL is a tool that detects cross-sample contamination in shotgun metagenomic data
  ☆24Updated this week
• broadinstitute / delphy
  Fast, scalable, accurate and accessible Bayesian phylogenetics
  ☆37Updated this week
• gtonkinhill / pairsnp
  A set of scripts for calculating pairwise SNP distance
  ☆40Updated 2 years ago
• hoelzer-lab / ribap
  A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPs
  ☆27Updated 6 months ago
• CFSAN-Biostatistics / C-WAP
  SC2 variant detection and composition pipeline
  ☆17Updated last year
• arumugamlab / msamtools
  Metagenomics-related extended functionalities to samtools
  ☆21Updated last year
• UPHL-BioNGS / Grandeur
  UPHL's Reference Free Pipeline
  ☆26Updated last week
• tseemann / scripts
  Miscellaneous Perl scripts from 20 years in microbial bioinformatics
  ☆17Updated 10 months ago
• chrisruis / MutTui
  MutTui pipeline to reconstruct mutational spectra for bacterial and viral datasets
  ☆29Updated 10 months ago
• Kalan-Lab / zol
  zol (& fai): large-scale targeted detection and evolutionary investigation of gene clusters (i.e. BGCs, phages, etc.)
  ☆59Updated 2 weeks ago
• jhuapl-bio / taxtriage
  TaxTriage is a Nextflow workflow designed to agnostically identify and classify microbial organisms within short- or long-read metagenomi…
  ☆34Updated this week
• lskatz / fundamentals-of-bioinformatics
  ☆17Updated this week
• tseemann / berokka
  🍊 💫 Trim, circularise and orient long read bacterial genome assemblies
  ☆26Updated 5 years ago
• noemielefrancq / Phylowave_Learning-fitness-dynamics-pathogens-in-phylogenies
  Code for the paper "Learning the fitness dynamics of pathogens from phylogenies"
  ☆17Updated 3 weeks ago
• iqtree / piqtree
  a python library that exposes features from iqtree2 - efficient software for phylogenomic inference
  ☆29Updated this week
• xavierdidelot / TransPhylo
  Reconstruction of transmission trees using genomic data
  ☆62Updated last year
• nextstrain / avian-flu
  Nextstrain build for avian influenza viruses
  ☆25Updated this week