Alternatives and similar repositories for PATO:

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

• jhawkey / IS_mapper
  IS mapping software
  ☆53Updated 3 years ago
• PombertLab / SYNY
  The SYNY pipeline investigates synteny between species by reconstructing protein clusters from gene pairs.
  ☆40Updated last week
• endixk / ezaai
  EzAAI - High Throughput Prokaryotic AAI Calculator
  ☆37Updated 3 months ago
• bhattlab / lathe
  A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing
  ☆69Updated 3 years ago
• zheminzhou / PEPPAN
  Phylogeny Enhanded Prediction of PAN-genome
  ☆40Updated 4 years ago
• Kalan-Lab / zol
  zol (& fai): large-scale targeted detection and evolutionary investigation of gene clusters (i.e. BGCs, phages, etc.)
  ☆51Updated last month
• SegataLab / panphlan
  PanPhlAn is a strain-level metagenomic profiling tool for identifying the gene composition of individual strains in metagenomic samples
  ☆44Updated last year
• EBI-Metagenomics / mettannotator
  ☆57Updated 3 weeks ago
• gtonkinhill / panstripe
  post processing of bacterial pangenome gene presence/absence matrices
  ☆54Updated 4 months ago
• bioinfo-ut / PlasmidSeeker
  A k-mer based program for the identification of known plasmids from whole-genome sequencing reads
  ☆35Updated 3 years ago
• shenwei356 / gtdb-taxdump
  GTDB taxonomy taxdump files with trackable TaxIds
  ☆51Updated 8 months ago
• mtisza1 / Cenote-Taker3
  Discover and annotate the virome
  ☆35Updated 3 months ago
• brinkmanlab / islandpath
  IslandPath standalone software
  ☆31Updated last year
• bvalot / pyMLST
  whole genome MLST analysis
  ☆40Updated 8 months ago
• DeniRibicic / q2ONT
  Bash pipeline for analysis of ONT full-length 16S sequences in QIIME2
  ☆28Updated 4 years ago
• xinehc / melon
  Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes
  ☆34Updated last month
• WatsonLab / MAGpy
  Snakemake pipeline for downstream analysis of metagenome-assembled genomes (MAGs) (pronounced mag-pie)
  ☆62Updated last year
• wandreopoulos / deeplasmid
  ☆18Updated 4 months ago
• philarevalo / PopCOGenT
  Microbial Populations as Clusters Of Gene Transfer
  ☆44Updated last year
• aldertzomer / RFPlasmid
  Predicting plasmid contigs from assemblies using single copy marker genes, plasmid genes, kmers - Developed by Linda van der Graaf
  ☆48Updated 9 months ago
• snayfach / MAGpurify
  Improvement of metagenome-assembled genomes
  ☆50Updated 4 years ago
• rrwick / Assembly-Dereplicator
  A tool for removing redundant genomes from a set of assemblies
  ☆70Updated last year
• weisberglab / beav
  BEAV: Bacterial Element Annotation reVamped
  ☆60Updated 2 months ago
• liaochenlanruo / pgcgap
  The Prokaryotic Genomics and Comparative Genomics Analysis Pipeline
  ☆38Updated 2 years ago
• rhysf / Synima
  Synteny Imager
  ☆60Updated 4 months ago
• mw55309 / ideel
  Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes
  ☆53Updated last year
• snayfach / MicrobeCensus
  MicrobeCensus estimates the average genome size of microbial communities from metagenomic data
  ☆43Updated 4 years ago
• allind / EukDetect
  ☆47Updated 9 months ago
• arumugamlab / msamtools
  Metagenomics-related extended functionalities to samtools
  ☆19Updated last year
• raw-lab / MetaCerberus
  Python code for versatile Functional Ontology Assignments for Metagenomes searching via Hidden Markov Model (HMM) with environmental focu…
  ☆53Updated 3 weeks ago