Alternatives and similar repositories for AAFTF

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

• weisberglab / beav
  BEAV: Bacterial Element Annotation reVamped
  ☆73Updated 5 months ago
• irycisBioinfo / PATO
  PATO is a R package designed to analyze pangenomes (set of genomes) intra or inter species.
  ☆63Updated 2 years ago
• microbial-pangenomes-lab / microGWAS
  Bacterial GWAS analysis
  ☆46Updated 3 weeks ago
• Kalan-Lab / zol
  zol (& fai): large-scale targeted detection and evolutionary investigation of gene clusters (i.e. BGCs, phages, etc.)
  ☆71Updated last month
• gtonkinhill / fastbaps
  A fast approximation to a Dirichlet Process Mixture model (DPM) for clustering genetic data
  ☆68Updated 3 years ago
• SWittouck / SCARAP
  A toolkit for prokaryotic comparative genomics
  ☆51Updated 3 months ago
• MrTomRod / scoary-2
  Calculate assocations between genes and traits
  ☆29Updated 11 months ago
• insapathogenomics / ReporTree
  A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data
  ☆47Updated 3 months ago
• wtmatlock / flanker
  Gene-flank analysis tool
  ☆37Updated last year
• vinuesa / get_phylomarkers
  A pipeline to select optimal markers for microbial phylogenomics and species tree estimation using the multispecies coalescent and concat…
  ☆60Updated 2 months ago
• rrwick / Assembly-Dereplicator
  A tool for removing redundant genomes from a set of assemblies
  ☆78Updated 5 months ago
• WatsonLab / MAGpy
  Snakemake pipeline for downstream analysis of metagenome-assembled genomes (MAGs) (pronounced mag-pie)
  ☆61Updated 2 years ago
• klebgenomics / Kaptive
  ☆57Updated last month
• CCB-SB / plsdb
  PLSDB pipeline to collect bacterial plasmids from NCBI
  ☆39Updated last year
• kussell-lab / mcorr
  Inferring bacterial recombination rates from large-scale sequencing datasets.
  ☆41Updated 2 years ago
• BenoitMorel / ParGenes
  A massively parallel tool for model selection and tree inference on thousands of genes
  ☆51Updated last year
• zheminzhou / PEPPAN
  Phylogeny Enhanded Prediction of PAN-genome
  ☆43Updated 5 years ago
• brinkmanlab / islandpath
  IslandPath standalone software
  ☆35Updated 2 years ago
• aldertzomer / RFPlasmid
  Predicting plasmid contigs from assemblies using single copy marker genes, plasmid genes, kmers - Developed by Linda van der Graaf
  ☆50Updated last year
• mtisza1 / Cenote-Taker3
  Discover and annotate the virome
  ☆58Updated this week
• philarevalo / PopCOGenT
  Microbial Populations as Clusters Of Gene Transfer
  ☆44Updated 2 years ago
• bvalot / pyMLST
  whole genome MLST analysis
  ☆51Updated 8 months ago
• flass / pantagruel
  a pipeline for reconciliation of phylogenetic histories within a bacterial pangenome
  ☆50Updated 3 years ago
• mw55309 / ideel
  Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes
  ☆54Updated 2 years ago
• bhattlab / lathe
  A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing
  ☆68Updated 4 years ago
• lmlui / Jorg
  MAG Circularization Method
  ☆32Updated 3 months ago
• rki-mf1 / clean
  A nextflow pipeline for decontamination of short reads, long reads and contigs
  ☆55Updated 7 months ago
• liaochenlanruo / pgcgap
  The Prokaryotic Genomics and Comparative Genomics Analysis Pipeline
  ☆41Updated 3 years ago
• rrwick / Verticall
  Recombination-free trees
  ☆63Updated 5 months ago
• AlexanderLabWHOI / EUKulele
  Automatic eukaryotic taxonomic classification
  ☆29Updated 9 months ago