Alternatives and similar repositories for treeWAS:

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

• MadsAlbertsen / multi-metagenome
  Scripts and tutorials on how to assemble individual microbial genomes from metagenomes
  ☆80Updated 8 years ago
• xavierdidelot / ClonalFrameML
  ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes
  ☆114Updated 10 months ago
• tobiasgf / lulu
  r package for post-clustering curation of amplicon next generation sequencing data (metabarcoding)
  ☆64Updated last year
• transcript / samsa2
  SAMSA pipeline, version 2.0. An open-source metatranscriptomics pipeline for analyzing microbiome data, built around DIAMOND and customi…
  ☆57Updated last year
• xavierdidelot / BactDating
  Bayesian inference of ancestral dates on bacterial phylogenetic trees
  ☆87Updated 5 months ago
• smdabdoub / kraken-biom
  Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWoo…
  ☆53Updated 3 years ago
• eead-csic-compbio / get_homologues
  GET_HOMOLOGUES: a versatile software package for pan-genome analysis
  ☆113Updated 3 weeks ago
• rrwick / Metagenomics-Index-Correction
  ☆81Updated last year
• nigyta / dfast_core
  DDBJ Fast Annotation and Submission Tool
  ☆79Updated last month
• gbouras13 / hybracter
  Automated long-read first bacterial genome assembly tool implemented in Snakemake using Snaketool.
  ☆121Updated 2 weeks ago
• HCBravoLab / metagenomeSeq
  Statistical analysis for sparse high-throughput sequencing
  ☆69Updated 3 months ago
• DeniRibicic / q2ONT
  Bash pipeline for analysis of ONT full-length 16S sequences in QIIME2
  ☆29Updated 5 years ago
• agmcfarland / r_phylogenetics_worshop
  Using ggtree to build phylogenetic trees
  ☆46Updated 4 months ago
• rhysf / Synima
  Synteny Imager
  ☆61Updated 7 months ago
• rrwick / Bacsort
  a collection of scripts for organising bacterial genomes by species
  ☆76Updated 3 years ago
• pierrebarbera / epa-ng
  Massively parallel phylogenetic placement of genetic sequences
  ☆82Updated 2 years ago
• rrwick / Autocycler
  A tool for generating consensus long-read assemblies for bacterial genomes
  ☆113Updated this week
• jhawkey / IS_mapper
  IS mapping software
  ☆53Updated 3 years ago
• donovan-h-parks / CompareM
  A toolbox for comparative genomics.
  ☆101Updated 3 years ago
• PacificBiosciences / HiFi-16S-workflow
  Nextflow pipeline to analyze PacBio HiFi full-length 16S data
  ☆71Updated last month
• jodyphelan / genomics_course
  ☆11Updated 2 weeks ago
• Sydney-Informatics-Hub / Shotgun-Metagenomics-Analysis
  Analysis of metagenomic shotgun sequences including assembly, speciation, ARG discovery and more
  ☆29Updated last year
• nmquijada / tormes
  Making whole bacterial genome sequencing data analysis easy
  ☆103Updated 4 months ago
• bhattlab / MGEfinder
  A toolbox for identifying mobile genetic element (MGE) insertions from short-read sequencing data of bacterial isolates.
  ☆116Updated last year
• moshi4 / COGclassifier
  A tool for classifying prokaryote protein sequences into COG(Cluster of Orthologous Genes) functional category
  ☆62Updated 6 months ago
• B-UMMI / chewBBACA
  BSR-Based Allele Calling Algorithm
  ☆141Updated 3 weeks ago
• bjtully / BioData
  All of my various bioinformatic scripts fit for public consumption (loosely defining "fit")
  ☆71Updated 2 years ago
• bacpop / PopPUNK
  PopPUNK 👨‍🎤 (POPulation Partitioning Using Nucleotide Kmers)
  ☆97Updated last week
• ParkinsonLab / Metatranscriptome-Workshop
  Metatranscriptomics Tutorial
  ☆62Updated last year
• patrickwest / EukRep
  Classification of Eukaryotic and Prokaryotic sequences from metagenomic datasets
  ☆69Updated 9 months ago