Alternatives and similar repositories for GToTree

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

• AdmiralenOla / Scoary
  Pan-genome wide association studies
  ☆205Updated last year
• MGXlab / CAT_pack
  CAT/BAT/RAT: tools for taxonomic classification of contigs and metagenome-assembled genomes (MAGs) and for taxonomic profiling of metage…
  ☆223Updated 2 weeks ago
• nf-core / taxprofiler
  Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
  ☆177Updated this week
• biobakery / phylophlan
  Precise phylogenetic analysis of microbial isolates and genomes from metagenomes
  ☆158Updated 7 months ago
• nickjcroucher / gubbins
  Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
  ☆211Updated 5 months ago
• CAMI-challenge / CAMISIM
  CAMISIM: Simulating metagenomes and microbial communities
  ☆221Updated this week
• B-UMMI / chewBBACA
  BSR-Based Allele Calling Algorithm
  ☆147Updated this week
• cruizperez / MicrobeAnnotator
  Pipeline for metabolic annotation of microbial genomes
  ☆150Updated 10 months ago
• gtonkinhill / panaroo
  An updated pipeline for pangenome investigation
  ☆339Updated 3 weeks ago
• bluenote-1577 / sylph
  ultrafast taxonomic profiling and genome querying for metagenomic samples by abundance-corrected minhash.
  ☆287Updated this week
• linnabrown / run_dbcan
  Run_dbcan V4, using genomes/metagenomes/proteomes of any assembled organisms (prokaryotes, fungi, plants, animals, viruses) to search for…
  ☆158Updated 9 months ago
• tseemann / barrnap
  Bacterial ribosomal RNA predictor
  ☆279Updated 3 weeks ago
• MrOlm / inStrain
  Bioinformatics program inStrain
  ☆181Updated 8 months ago
• PacificBiosciences / pb-metagenomics-tools
  Tools and pipelines tailored to using PacBio HiFi Reads for metagenomics
  ☆199Updated 4 months ago
• cmks / DAS_Tool
  DAS Tool
  ☆168Updated last year
• labgem / PPanGGOLiN
  Build a partitioned pangenome graph from microbial genomes
  ☆292Updated last month
• tseemann / any2fasta
  Convert various sequence formats to FASTA
  ☆146Updated last month
• phac-nml / staramr
  Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.
  ☆183Updated this week
• DRL / blobtools
  Modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets
  ☆208Updated last year
• neherlab / pan-genome-analysis
  Processing pipeline for pan-genome visulization and exploration
  ☆143Updated 2 years ago
• katholt / srst2
  Short Read Sequence Typing for Bacterial Pathogens
  ☆145Updated 4 years ago
• sanger-pathogens / circlator
  A tool to circularize genome assemblies
  ☆251Updated last year
• kblin / ncbi-acc-download
  Download files from NCBI Entrez by accession
  ☆134Updated last year
• pha4ge / hAMRonization
  Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure
  ☆173Updated 2 months ago
• AnantharamanLab / VIBRANT
  Virus Identification By iteRative ANnoTation
  ☆184Updated last year
• bluenote-1577 / skani
  Fast, robust ANI and aligned fraction for (metagenomic) genomes and contigs.
  ☆234Updated 3 months ago
• chklovski / CheckM2
  Assessing the quality of metagenome-derived genome bins using machine learning
  ☆247Updated 10 months ago
• tseemann / shovill
  ⚡♠️ Assemble bacterial isolate genomes from Illumina paired-end reads
  ☆252Updated last month
• biobakery / biobakery_workflows
  bioBakery workflows is a collection of workflows and tasks for executing common microbial community analyses using standardized, validate…
  ☆129Updated 3 months ago
• rrwick / Trycycler
  A tool for generating consensus long-read assemblies for bacterial genomes
  ☆338Updated 4 months ago