Alternatives and similar repositories for IQ-TREE

Users that are interested in IQ-TREE are comparing it to the libraries listed below

• rrwick / Trycycler
  A tool for generating consensus long-read assemblies for bacterial genomes
  ☆320Updated 11 months ago
• schneebergerlab / plotsr
  Tool to plot synteny and structural rearrangements between genomes
  ☆303Updated last month
• DRL / blobtools
  Modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets
  ☆201Updated 8 months ago
• iqtree / iqtree2
  IQ-TREE software version 2: phylogenetics by maximum likelihood
  ☆285Updated 2 weeks ago
• sanger-pathogens / circlator
  A tool to circularize genome assemblies
  ☆242Updated last year
• ndierckx / NOVOPlasty
  NOVOPlasty - The organelle assembler and heteroplasmy caller
  ☆187Updated last year
• jtlovell / GENESPACE
  ☆208Updated 3 months ago
• alekseyzimin / masurca
  ☆255Updated last week
• tseemann / barrnap
  Bacterial ribosomal RNA predictor
  ☆243Updated last year
• rrwick / Long-read-assembler-comparison
  Benchmarking of long-read assembly tools for bacterial whole genomes
  ☆171Updated 4 years ago
• tseemann / shovill
  ⚡♠️ Assemble bacterial isolate genomes from Illumina paired-end reads
  ☆223Updated 2 years ago
• B-UMMI / chewBBACA
  BSR-Based Allele Calling Algorithm
  ☆143Updated last month
• inab / trimal
  A tool for automated alignment trimming in large-scale phylogenetic analyses. Development version: 2.0
  ☆203Updated this week
• simonhmartin / genomics_general
  General tools for genomic analyses.
  ☆360Updated 2 months ago
• Nextomics / NextPolish
  Fast and accurately polish the genome generated by long reads.
  ☆223Updated 4 months ago
• linzhi2013 / MitoZ
  MitoZ: A toolkit for assembly, annotation, and visualization of animal mitochondrial genomes
  ☆123Updated 6 months ago
• roblanf / minion_qc
  Quality control for MinION sequencing data
  ☆217Updated 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…
  ☆309Updated 2 months ago
• mossmatters / HybPiper
  Recovering genes from targeted sequence capture data
  ☆121Updated 4 months ago
• abacus-gene / paml
  PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. Please report only **techni…
  ☆152Updated this week
• AstrobioMike / GToTree
  A user-friendly workflow for phylogenomics
  ☆213Updated this week
• nextgenusfs / funannotate
  Eukaryotic Genome Annotation Pipeline
  ☆349Updated 2 months ago
• rrwick / Filtlong
  quality filtering tool for long reads
  ☆329Updated last year
• eead-csic-compbio / get_homologues
  GET_HOMOLOGUES: a versatile software package for pan-genome analysis
  ☆115Updated 2 months ago
• malonge / RaGOO
  RaGOO is no longer supported. Please use RagTag instead: https://github.com/malonge/RagTag
  ☆173Updated 3 years ago
• tseemann / nullarbor
  "Reads to report" for public health and clinical microbiology
  ☆139Updated last year
• hahnlab / CAFE
  Analyze changes in gene family size and provide a statistical foundation for evolutionary inferences.
  ☆116Updated 4 years ago
• tseemann / any2fasta
  Convert various sequence formats to FASTA
  ☆135Updated 2 years ago
• schatzlab / genomescope
  Fast genome analysis from unassembled short reads
  ☆290Updated last year
• millanek / Dsuite
  Fast calculation of Patterson's D (ABBA-BABA) and the f4-ratio statistics across many populations/species
  ☆172Updated 4 months ago