Alternatives and similar repositories for civet

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

• xavierdidelot / TransPhylo
  Reconstruction of transmission trees using genomic data
  ☆72Updated 2 years ago
• BDI-pathogens / phyloscanner
  Phylogenetics between and within hosts at once, all along the genome.
  ☆50Updated last year
• PoonLab / covizu
  Rapid analysis and visualization of coronavirus genome variation
  ☆48Updated 2 weeks ago
• jts / ncov-tools
  Small collection of tools for performing quality control on coronavirus sequencing data and genomes
  ☆49Updated last year
• andersen-lab / avian-influenza
  Consensus sequences for U.S. H5N1 clade 2.3.4.4b
  ☆37Updated this week
• GATB / simka
  Simka and SimkaMin are comparative metagenomics methods dedicated to NGS datasets.
  ☆51Updated 4 years ago
• emvolz / treedater
  Scalable relaxed clock phylogenetic dating
  ☆28Updated 5 months ago
• ukhsa-collaboration / variant_definitions
  ☆74Updated 2 years ago
• CDCgov / tostadas
  🧬 💻 TOSTADAS → Toolkit for Open Sequence Triage, Annotation and DAtabase Submission
  ☆28Updated 4 months ago
• gtonkinhill / rhierbaps
  rhierbaps: R implementation of hierBAPS
  ☆37Updated 4 years ago
• gtonkinhill / pairsnp
  A set of scripts for calculating pairwise SNP distance
  ☆44Updated 3 years ago
• blaxterlab / blobology
  Tools for making blobplots or Taxon-Annotated-GC-Coverage plots (TAGC plots) to visualise the contents of genome assembly data sets as a …
  ☆47Updated 3 years ago
• jhuapl-bio / taxtriage
  TaxTriage is a Nextflow workflow designed to agnostically identify and classify microbial organisms within short- or long-read metagenomi…
  ☆61Updated this week
• sanger-pathogens / iva
  de novo virus assembler of Illumina paired reads
  ☆58Updated 4 years ago
• roblanf / sarscov2phylo
  Global phylogenies of SARS-CoV-2 sequences
  ☆85Updated 2 years ago
• flass / pantagruel
  a pipeline for reconciliation of phylogenetic histories within a bacterial pangenome
  ☆50Updated 3 years ago
• sanger-pathogens / gff3toembl
  Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI
  ☆29Updated 7 years ago
• ukhsa-collaboration / PHEnix
  Public Health England SNP calling pipeline.
  ☆37Updated 7 years ago
• maximilianh / multiSub
  Prepares a SARS-CoV-2 submission for GISAID, NCBI or ENA. Can read GISAID or NCBI files, or plain fasta+tsv/csv/xls. Finds files in input…
  ☆36Updated 3 years ago
• hsgweon / pipits
  Automated pipeline for analyses of fungal ITS from the Illumina
  ☆32Updated 9 months ago
• flu-crew / parnas
  Phylogenetic maximum representation sampling: choosing most representative strains or taxa
  ☆40Updated 4 months ago
• pha4ge / pipeline-resources
  Bioinformatics Pipeline and Visualization resources
  ☆60Updated last year
• emvolz-phylodynamics / treestructure
  ☆18Updated 4 months ago
• tseemann / ekidna
  Assembly based core genome SNP alignments for bacteria
  ☆25Updated 6 years ago
• gtonkinhill / fastbaps
  A fast approximation to a Dirichlet Process Mixture model (DPM) for clustering genetic data
  ☆68Updated 3 years ago
• snayfach / IGGsearch
  Metagenomic species profiling with enhanced coverage of the human gut microbiome
  ☆25Updated last year
• USDA-VS / GenoFLU
  Influenza data pipeline to automate genotyping assignment
  ☆39Updated 3 months ago
• ncbi / rapt
  This RAPT repository has been retired as of December 2024. NCBI's Read assembly and Annotation Pipeline Tool (RAPT) was a pilot service.
  ☆58Updated 10 months ago
• achtman-lab / GrapeTree
  GrapeTree is a fully interactive, tree visualization program, which supports facile manipulations of both tree layout and metadata. Click…
  ☆86Updated last year
• andersgs / harrietr
  An `R` package for various phylogenetic and evolutionary biology data manipulations
  ☆12Updated 7 years ago