Alternatives and similar repositories for megan-ce

Users that are interested in megan-ce are comparing it to the libraries listed below

• KorfLab / CEGMA_v2

  View on GitHub
  The final version 2 release of our software to detect core genes in eukaryotic genomes
  ☆29Mar 31, 2015Updated 10 years ago
• merenlab / merenlab.org

  View on GitHub
  Web content for Meren Lab
  ☆11Feb 7, 2026Updated last week
• jbloomlab / alignparse

  View on GitHub
  Align sequences and then parse features.
  ☆17Oct 24, 2025Updated 3 months ago
• peterjc / thapbi-pict

  View on GitHub
  Tree Health and Plant Biosecurity Initiative - Phytophthora ITS1 Classifier Tool
  ☆10Feb 2, 2026Updated last week
• dfguan / rHAT

  View on GitHub
  Pacbio sequence alignment tool, please use "git clone" to copy and use the repository
  ☆18Feb 17, 2019Updated 6 years ago
• camillescott / shmlast

  View on GitHub
  blast, shmlast
  ☆21Oct 5, 2020Updated 5 years ago
• freestatman / ideogRam

  View on GitHub
  R htmlwidget package for ideogram.js
  ☆15Oct 26, 2022Updated 3 years ago
• iqbal-lab-org / pandora

  View on GitHub
  Pan-genome inference and genotyping with long noisy or short accurate reads
  ☆119Dec 13, 2024Updated last year
• taxoniq / taxoniq

  View on GitHub
  Taxon Information Query - fast, offline querying of NCBI Taxonomy and related data
  ☆59Sep 19, 2024Updated last year
• HuntsmanCancerInstitute / USeq

  View on GitHub
  180+ Java applications for analyzing next generation sequencing data from ChIPSeq, RNASeq, BisSeq, DNASeq, variant annotation/ filtering,…
  ☆18Nov 6, 2025Updated 3 months ago
• DaehwanKimLab / centrifuge

  View on GitHub
  Classifier for metagenomic sequences
  ☆270Jun 20, 2025Updated 7 months ago
• YuLab-SMU / ggtreeDendro

  View on GitHub
  Drawing 'dendrogram' using 'ggtree'
  ☆13Nov 1, 2025Updated 3 months ago
• alk224 / akutils-v1.1.1

  View on GitHub
  Mostly useful scripts and files for processing MiSeq amplicon data
  ☆18Jul 1, 2016Updated 9 years ago
• aquaskyline / SOAPdenovo2

  View on GitHub
  Next generation sequencing reads de novo assembler.
  ☆239Sep 20, 2025Updated 4 months ago
• bbuchfink / diamond

  View on GitHub
  Accelerated BLAST compatible local sequence aligner.
  ☆1,239Feb 7, 2026Updated last week
• merenlab / oligotyping

  View on GitHub
  Exploring microbial patterns through subtle nucleotide variation within 16S rRNA gene tag sequences of closely related taxa
  ☆41Jun 24, 2024Updated last year
• bokulich-lab / RESCRIPt

  View on GitHub
  REference Sequence annotation and CuRatIon Pipeline
  ☆98Updated this week
• nanoporetech / minimappy

  View on GitHub
  Python bindings to minimap2
  ☆16Sep 18, 2017Updated 8 years ago
• mjsull / Contiguity

  View on GitHub
  Tool for visualising assemblies.
  ☆17Sep 15, 2015Updated 10 years ago
• desmid / mview

  View on GitHub
  MView extracts and reformats the results of a sequence database search or multiple alignment.
  ☆33Sep 8, 2024Updated last year
• mothur / mothur

  View on GitHub
  Welcome to the mothur project, initiated by Dr. Patrick Schloss and his software development team in the Department of Microbiology & Imm…
  ☆276Jan 13, 2026Updated last month
• fbreitwieser / pavian

  View on GitHub
  🌈 Interactive analysis of metagenomics data
  ☆442Sep 17, 2025Updated 4 months ago
• jltsiren / gcsa2

  View on GitHub
  BWT-based index for graphs
  ☆73Mar 12, 2025Updated 11 months ago
• bcgsc / abyss

  View on GitHub
  Assemble large genomes using short reads
  ☆327Mar 27, 2025Updated 10 months ago
• edawson / gfakluge

  View on GitHub
  A C++ library and utilities for manipulating the Graphical Fragment Assembly format.
  ☆55May 17, 2022Updated 3 years ago
• hallamlab / metapathways2

  View on GitHub
  MetaPathways v2.0: A master-worker model for environmental Pathway/Genome Database construction on grids and clouds
  ☆33Nov 26, 2015Updated 10 years ago
• iqbal-lab / Mykrobe-predictor

  View on GitHub
  Antibiotic resistance predictions in minutes on a laptop
  ☆50Mar 7, 2019Updated 6 years ago
• caballero / SeqComplex

  View on GitHub
  Algorithms to compute DNA complexity
  ☆35May 24, 2022Updated 3 years ago
• marbl / Krona

  View on GitHub
  Interactively explore metagenomes and more from a web browser.
  ☆493Dec 22, 2021Updated 4 years ago
• Kingsford-Group / bloomtree

  View on GitHub
  ☆73Mar 1, 2019Updated 6 years ago
• biocore / qiime

  View on GitHub
  Official QIIME 1 software repository. QIIME 2 (https://qiime2.org) has succeeded QIIME 1 as of January 2018.
  ☆285Dec 19, 2022Updated 3 years ago
• MG-RAST / pipeline

  View on GitHub
  The MG-RAST pipeline
  ☆25Nov 30, 2022Updated 3 years ago
• karel-brinda / Phylign

  View on GitHub
  Alignment against all pre-2019 bacteria on laptops within a few hours (former MOF-Search)
  ☆41Apr 17, 2024Updated last year
• caporaso-lab / mockrobiota

  View on GitHub
  A public resource for microbiome bioinformatics benchmarking using artificially constructed (i.e., mock) communities.
  ☆83May 14, 2019Updated 6 years ago
• caitiecollins / treeWAS

  View on GitHub
  treeWAS: A Phylogenetic Tree-Based Tool for Genome-Wide Association Studies in Microbes
  ☆106Feb 6, 2025Updated last year
• biobakery / biobakery

  View on GitHub
  bioBakery tools for meta'omic profiling
  ☆305Jun 3, 2025Updated 8 months ago
• zhaoyanswill / RAPSearch2

  View on GitHub
  Reduced Alphabet based Protein similarity Search
  ☆40Nov 30, 2020Updated 5 years ago
• Shamir-Lab / Recycler

  View on GitHub
  This is the codebase for Recycler, described in our manuscript: https://academic.oup.com/bioinformatics/article/33/4/475/2623362, by Roye…
  ☆58Apr 22, 2021Updated 4 years ago
• mummer4 / mummer

  View on GitHub
  Mummer alignment tool
  ☆548Feb 4, 2025Updated last year