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
  ☆63Updated last year
• BDI-pathogens / phyloscanner
  Phylogenetics between and within hosts at once, all along the genome.
  ☆50Updated 10 months ago
• gtonkinhill / rhierbaps
  rhierbaps: R implementation of hierBAPS
  ☆35Updated 4 years ago
• GATB / simka
  Simka and SimkaMin are comparative metagenomics methods dedicated to NGS datasets.
  ☆48Updated 3 years ago
• roblanf / sarscov2phylo
  Global phylogenies of SARS-CoV-2 sequences
  ☆86Updated last year
• flass / pantagruel
  a pipeline for reconciliation of phylogenetic histories within a bacterial pangenome
  ☆49Updated 2 years ago
• ukhsa-collaboration / variant_definitions
  ☆74Updated last year
• gtonkinhill / pairsnp
  A set of scripts for calculating pairwise SNP distance
  ☆42Updated 2 years ago
• PoonLab / covizu
  Rapid analysis and visualization of coronavirus genome variation
  ☆48Updated 3 weeks ago
• jts / ncov-tools
  Small collection of tools for performing quality control on coronavirus sequencing data and genomes
  ☆48Updated last year
• emvolz / treedater
  Scalable relaxed clock phylogenetic dating
  ☆25Updated last week
• gtonkinhill / fastbaps
  A fast approximation to a Dirichlet Process Mixture model (DPM) for clustering genetic data
  ☆64Updated 2 years ago
• xavierdidelot / BactDating
  Bayesian inference of ancestral dates on bacterial phylogenetic trees
  ☆90Updated this week
• pha4ge / pipeline-resources
  Bioinformatics Pipeline and Visualization resources
  ☆57Updated 11 months ago
• sanger-pathogens / iva
  de novo virus assembler of Illumina paired reads
  ☆56Updated 4 years ago
• richardmleggett / MARTi
  Metagenomic Analysis in Real Time
  ☆24Updated this week
• jhuapl-bio / taxtriage
  TaxTriage is a Nextflow workflow designed to agnostically identify and classify microbial organisms within short- or long-read metagenomi…
  ☆55Updated last month
• cov-lineages / pangolin-data
  Repository for storing latest model, protobuf, designation hash and alias files for pangolin assignments
  ☆31Updated last month
• 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 4 months ago
• tseemann / cgmlst-dists
  🐻⇔🐨 Calculate distance matrix from ChewBBACA cgMLST allele call tables
  ☆28Updated last year
• andersgs / harrietr
  An `R` package for various phylogenetic and evolutionary biology data manipulations
  ☆12Updated 7 years ago
• achtman-lab / GrapeTree
  GrapeTree is a fully interactive, tree visualization program, which supports facile manipulations of both tree layout and metadata. Click…
  ☆83Updated 7 months ago
• dib-lab / genome-grist
  map Illumina metagenomes to genomes!
  ☆39Updated last month
• 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
• CDCgov / datasets-sars-cov-2
  Benchmark datasets for WGS analysis of SARS-CoV-2. (https://peerj.com/articles/13821/)
  ☆56Updated 2 years ago
• INSaFLU / INSaFLU
  INSaFLU-TELEVIR: an free web-based (but also locally installable) bioinformatics suite for virus metagenomic detection and routine genomi…
  ☆37Updated this week
• andrewjpage / tiptoft
  Predict plasmids from uncorrected long read data
  ☆40Updated 5 years ago
• sdwfrost / gbmunge
  Munge GenBank files into FASTA and tab-separated metadata
  ☆14Updated last year
• bacpop / PopPUNK
  PopPUNK 👨‍🎤 (POPulation Partitioning Using Nucleotide Kmers)
  ☆100Updated last week
• andersen-lab / avian-influenza
  Consensus sequences for U.S. H5N1 clade 2.3.4.4b
  ☆34Updated last week