Alternatives and similar repositories for twilight:

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

• raw-lab / MetaCerberus
  Python code for versatile Functional Ontology Assignments for Metagenomes searching via Hidden Markov Model (HMM) with environmental focu…
  ☆53Updated last month
• gtonkinhill / panstripe
  post processing of bacterial pangenome gene presence/absence matrices
  ☆54Updated 5 months ago
• gbouras13 / dnaapler
  Reorients assembled microbial sequences
  ☆107Updated 2 weeks ago
• gbouras13 / plassembler
  Program to quickly and accurately assemble plasmids in hybrid and long-only sequenced bacterial isolates
  ☆58Updated 2 weeks ago
• Kalan-Lab / zol
  zol (& fai): large-scale targeted detection and evolutionary investigation of gene clusters (i.e. BGCs, phages, etc.)
  ☆52Updated last month
• endixk / ezaai
  EzAAI - High Throughput Prokaryotic AAI Calculator
  ☆37Updated 3 months ago
• moshi4 / COGclassifier
  A tool for classifying prokaryote protein sequences into COG(Cluster of Orthologous Genes) functional category
  ☆59Updated 4 months ago
• 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
• rrwick / Autocycler
  A tool for generating consensus long-read assemblies for bacterial genomes
  ☆93Updated last week
• cultivarium / MicrobeMod
  A toolkit for exploring prokaryotic methylation and base modifications in nanopore sequencing
  ☆44Updated last week
• AnantharamanLab / vRhyme
  Binning Virus Genomes from Metagenomes
  ☆59Updated 2 years ago
• adamhockenberry / bacphlip
  A python library for predicting phage lifestyle based on genome sequence
  ☆35Updated last year
• allind / EukDetect
  ☆48Updated 9 months ago
• kussell-lab / mcorr
  Inferring bacterial recombination rates from large-scale sequencing datasets.
  ☆42Updated last year
• KatariinaParnanen / MobileGeneticElementDatabase
  Contains a fasta format database of a large variety of mobile genetic elements and an annotation file
  ☆43Updated 3 years ago
• mtisza1 / Cenote-Taker3
  Discover and annotate the virome
  ☆35Updated 3 months ago
• linsalrob / PhiSpy
  Prediction of prophages from bacterial genomes
  ☆74Updated last year
• shenwei356 / gtdb-taxdump
  GTDB taxonomy taxdump files with trackable TaxIds
  ☆51Updated 9 months ago
• gem-pasteur / PanACoTA
  PANgenome with Annotations, COre identification, Tree and corresponding Alignments
  ☆73Updated last year
• gatech-genemark / MetaGeneMark-2
  MetaGeneMark-2: Improved Gene Prediction in Metagenomes
  ☆18Updated 10 months ago
• bacpop / ggCaller
  Bifrost graph gene caller.
  ☆91Updated 4 months ago
• BenoitMorel / GeneRax
  ☆70Updated last year
• rrwick / Verticall
  Recombination-free trees
  ☆56Updated last year
• patrickwest / EukRep_Pipeline
  ☆24Updated 6 years ago
• irycisBioinfo / PATO
  PATO is a R package designed to analyze pangenomes (set of genomes) intra or inter species.
  ☆58Updated last year
• EBI-Metagenomics / EukCC
  Tool to estimate genome quality of microbial eukaryotes
  ☆35Updated last week
• ac1513 / MAGqual
  MAGqual is a command line tool to evaluate the quality of metagenomic bins and generate recommended metadata in line with the MIMAG stand…
  ☆13Updated 5 months ago
• mw55309 / ideel
  Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes
  ☆53Updated last year
• nekokoe / Plasmer
  An accurate and sensitive bacterial plasmid identification tool based on deep machine-learning of shared k-mers and genomic features.
  ☆42Updated last year
• brinkmanlab / islandpath
  IslandPath standalone software
  ☆31Updated last year