Alternatives and similar repositories for hyphy:

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

• nextgenusfs / funannotate
  Eukaryotic Genome Annotation Pipeline
  ☆333Updated last month
• sanger-pathogens / circlator
  A tool to circularize genome assemblies
  ☆237Updated 10 months ago
• Dfam-consortium / RepeatMasker
  RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.
  ☆244Updated 3 months ago
• tseemann / barrnap
  Bacterial ribosomal RNA predictor
  ☆236Updated last year
• barricklab / breseq
  breseq is a computational pipeline for finding mutations relative to a reference sequence in short-read DNA resequencing data. It is inte…
  ☆157Updated last month
• TransDecoder / TransDecoder
  TransDecoder source
  ☆285Updated 5 months ago
• NBISweden / GAAS
  Genome Assembly and Annotation Service code
  ☆208Updated last year
• schneebergerlab / syri
  Synteny and Rearrangement Identifier
  ☆364Updated last week
• ndierckx / NOVOPlasty
  NOVOPlasty - The organelle assembler and heteroplasmy caller
  ☆183Updated last year
• ncbi / pgap
  NCBI Prokaryotic Genome Annotation Pipeline
  ☆328Updated last month
• arpcard / rgi
  Resistance Gene Identifier (RGI). Software to predict resistomes from protein or nucleotide data, including metagenomics data, based on h…
  ☆351Updated this week
• broadinstitute / pilon
  Pilon is an automated genome assembly improvement and variant detection tool
  ☆348Updated 2 years ago
• rrwick / Trycycler
  A tool for generating consensus long-read assemblies for bacterial genomes
  ☆315Updated 9 months ago
• rrwick / Filtlong
  quality filtering tool for long reads
  ☆322Updated last year
• gtonkinhill / panaroo
  An updated pipeline for pangenome investigation
  ☆283Updated this week
• a-slide / pycoQC
  pycoQC computes metrics and generates Interactive QC plots from the sequencing summary report generated by Oxford Nanopore technologies b…
  ☆276Updated 4 months ago
• wdecoster / nanofilt
  Filtering and trimming of long read sequencing data
  ☆201Updated 2 years ago
• Gaius-Augustus / BRAKER
  BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET/EP/ETP and AUGUSTUS in novel eu…
  ☆381Updated last month
• DRL / blobtools
  Modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets
  ☆197Updated 6 months ago
• marbl / verkko
  Telomere-to-telomere assembly of accurate long reads (PacBio HiFi, Oxford Nanopore Duplex, HERRO corrected Oxford Nanopore Simplex) and O…
  ☆320Updated this week
• tseemann / shovill
  ⚡♠️ Assemble bacterial isolate genomes from Illumina paired-end reads
  ☆218Updated 2 years ago
• Gaius-Augustus / Augustus
  Genome annotation with AUGUSTUS
  ☆294Updated last month
• abacus-gene / paml
  PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. Please report only **techni…
  ☆140Updated last month
• nf-core / nanoseq
  Nanopore demultiplexing, QC and alignment pipeline
  ☆195Updated last month
• malonge / RagTag
  Tools for fast and flexible genome assembly scaffolding and improvement
  ☆492Updated last year
• iqtree / iqtree2
  NEW location of IQ-TREE software for efficient phylogenomic software by maximum likelihood http://www.iqtree.org
  ☆268Updated this week
• sanger-pathogens / Roary
  Rapid large-scale prokaryote pan genome analysis
  ☆335Updated 2 years ago
• jenniferlu717 / Bracken
  Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species i…
  ☆303Updated this week
• AstrobioMike / GToTree
  A user-friendly workflow for phylogenomics
  ☆206Updated last week
• metagenome-atlas / atlas
  ATLAS - Three commands to start analyzing your metagenome data
  ☆383Updated 2 months ago