Alternatives and similar repositories for mafTools:

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

• sujaikumar / assemblage
  Tools for working with second gen assemblies, fasta sequences, etc
  ☆92Updated 8 years ago
• wurmlab / flo
  Same species annotation lift over pipeline.
  ☆96Updated last year
• bergmanlab / mcclintock
  Meta-pipeline to identify transposable element insertions using next generation sequencing data
  ☆95Updated last year
• voichek / kmersGWAS
  A library for running k-mers based GWAS
  ☆106Updated 3 months ago
• dwinter / pafr
  Read, manipulate and visualize 'Pairwise mApping Format' data in R
  ☆71Updated 3 years ago
• RemiAllio / MitoFinder
  MitoFinder: efficient automated large-scale extraction of mitogenomic data from high throughput sequencing data
  ☆93Updated 9 months ago
• JimWhiting91 / genotype_plot
  A set of functions to visualise genotypes based on a VCF
  ☆85Updated 3 years ago
• rhysf / Synima
  Synteny Imager
  ☆60Updated 5 months ago
• xiaochuanle / MECAT2
  ☆70Updated 4 years ago
• tobiasrausch / wally
  Wally: Visualization of aligned sequencing reads and contigs
  ☆111Updated last month
• zhangrengang / TEsorter
  TEsorter: an accurate and fast method to classify LTR-retrotransposons in plant genomes
  ☆90Updated last week
• malonge / RaGOO
  RaGOO is no longer supported. Please use RagTag instead: https://github.com/malonge/RagTag
  ☆172Updated 3 years ago
• ArimaGenomics / mapping_pipeline
  Mapping pipeline for data generated using Arima-HiC
  ☆71Updated 8 months ago
• 4ureliek / Parsing-RepeatMasker-Outputs
  Few scripts facilitating the extraction of info from Repeat Masker .out files
  ☆78Updated 3 years ago
• tbenavi1 / genomescope2.0
  Reference-free profiling of polyploid genomes
  ☆112Updated 6 months ago
• enormandeau / gawn
  Genome Annotation Without Nightmares
  ☆43Updated last week
• thlee / SNPhylo
  A pipeline to generate a phylogenetic tree from huge SNP data
  ☆86Updated last year
• glennhickey / progressiveCactus
  Distribution package for the Prgressive Cactus multiple genome aligner. Dependencies are linked as submodules
  ☆84Updated 6 years ago
• marbl / SALSA
  SALSA: A tool to scaffold long read assemblies with Hi-C data
  ☆183Updated 8 months ago
• kiranbandi / synvisio
  SynVisio is an interactive multiscale visualization tool that lets you explore the results of McScanX a popular synteny and collinearity …
  ☆82Updated 11 months ago
• steuernb / NLR-Annotator
  NLR-Annotator upload
  ☆62Updated last year
• marbl / ModDotPlot
  ☆126Updated 3 months ago
• Oshlack / Lace
  Building SuperTranscripts: A linear representation of transcriptome data
  ☆67Updated 3 years ago
• BGI-shenzhen / RectChr
  Multi-level visualization of genomic statistical variables on rectangular chromosomes
  ☆85Updated 2 months ago
• nanoporetech / pychopper
  A tool to identify, orient, trim and rescue full length cDNA reads
  ☆81Updated 2 years ago
• BioInf-Wuerzburg / proovread
  PacBio hybrid error correction through iterative short read consensus
  ☆60Updated 5 years ago
• clemgoub / dnaPipeTE
  dnaPipeTE (for de-novo assembly & annotation Pipeline for Transposable Elements), is a pipeline designed to find, annotate and quantify T…
  ☆52Updated last year
• HuffordLab / NAM-genomes
  Detailed bioinformatics scripts and methods used in the NAM genome paper.
  ☆74Updated 2 weeks ago
• EichlerLab / pav
  Phased assembly variant caller
  ☆107Updated last month
• PacificBiosciences / pb-CpG-tools
  Collection of tools for the analysis of CpG data
  ☆76Updated this week