Alternatives and similar repositories for hyphy

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

• sanger-pathogens / circlator
  A tool to circularize genome assemblies
  ☆248Updated last year
• barricklab / breseq
  breseq is a computational pipeline for finding mutations relative to a reference sequence using high-throughput DNA resequencing data. It…
  ☆172Updated 3 months ago
• tseemann / barrnap
  Bacterial ribosomal RNA predictor
  ☆259Updated 2 years ago
• AdmiralenOla / Scoary
  Pan-genome wide association studies
  ☆204Updated last year
• nextgenusfs / funannotate
  Eukaryotic Genome Annotation Pipeline
  ☆366Updated 3 months ago
• inab / trimal
  A tool for automated alignment trimming in large-scale phylogenetic analyses. Development version: 2.0
  ☆231Updated this week
• gtonkinhill / panaroo
  An updated pipeline for pangenome investigation
  ☆317Updated 8 months ago
• Gaius-Augustus / Augustus
  Genome annotation with AUGUSTUS
  ☆320Updated 2 months ago
• AstrobioMike / GToTree
  A user-friendly workflow for phylogenomics
  ☆221Updated last week
• schatzlab / genomescope
  Fast genome analysis from unassembled short reads
  ☆299Updated last year
• NBISweden / GAAS
  Genome Assembly and Annotation Service code
  ☆216Updated last year
• Dfam-consortium / RepeatMasker
  RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.
  ☆276Updated 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…
  ☆174Updated last month
• BioInfoTools / BBMap
  (Not Offical) BBMap short read aligner, and other bioinformatic tools.
  ☆242Updated 4 years ago
• fbreitwieser / krakenuniq
  🐙 KrakenUniq: Metagenomics classifier with unique k-mer counting for more specific results
  ☆240Updated last year
• ndierckx / NOVOPlasty
  NOVOPlasty - The organelle assembler and heteroplasmy caller
  ☆193Updated last year
• labgem / PPanGGOLiN
  Build a partitioned pangenome graph from microbial genomes
  ☆284Updated this week
• sortmerna / sortmerna
  SortMeRNA: next-generation sequence filtering and alignment tool
  ☆277Updated 2 months ago
• broadinstitute / pilon
  Pilon is an automated genome assembly improvement and variant detection tool
  ☆369Updated 3 years ago
• rrwick / Trycycler
  A tool for generating consensus long-read assemblies for bacterial genomes
  ☆333Updated last month
• AliView / AliView
  Software for aligning viewing and editing dna/aminoacid sequences, intuitive, fast and lightweight. Download and website:
  ☆142Updated 7 months ago
• tseemann / any2fasta
  Convert various sequence formats to FASTA
  ☆138Updated 3 years ago
• tseemann / shovill
  ⚡♠️ Assemble bacterial isolate genomes from Illumina paired-end reads
  ☆237Updated 2 years ago
• DaehwanKimLab / centrifuge
  Classifier for metagenomic sequences
  ☆266Updated 4 months ago
• schneebergerlab / plotsr
  Tool to plot synteny and structural rearrangements between genomes
  ☆326Updated 6 months ago
• katholt / srst2
  Short Read Sequence Typing for Bacterial Pathogens
  ☆139Updated 4 years ago
• nf-core / mag
  Assembly and binning of metagenomes
  ☆249Updated last week
• DRL / blobtools
  Modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets
  ☆207Updated last year
• nf-core / taxprofiler
  Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
  ☆168Updated this week
• daler / gffutils
  GFF and GTF file manipulation and interconversion
  ☆308Updated last year