Alternatives and similar repositories for angsd

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

• edgardomortiz / vcf2phylip
  Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis
  ☆327Updated 2 years ago
• lh3 / psmc
  Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model
  ☆183Updated 2 months ago
• KamilSJaron / smudgeplot
  Inference of ploidy and heterozygosity structure using whole genome sequencing data
  ☆291Updated last week
• ndierckx / NOVOPlasty
  NOVOPlasty - The organelle assembler and heteroplasmy caller
  ☆195Updated 2 years ago
• NBISweden / GAAS
  Genome Assembly and Annotation Service code
  ☆217Updated 2 years ago
• PASApipeline / PASApipeline
  PASA software
  ☆197Updated 11 months ago
• wdecoster / nanofilt
  Filtering and trimming of long read sequencing data
  ☆213Updated 3 years ago
• popgenmethods / smcpp
  SMC++ infers population history from whole-genome sequence data.
  ☆172Updated 2 years ago
• Dfam-consortium / RepeatModeler
  De-Novo Repeat Discovery Tool
  ☆229Updated 6 months ago
• tpoorten / dotPlotly
  Generate an interactive dot plot from mummer or minimap alignments
  ☆210Updated 2 years ago
• oushujun / LTR_retriever
  LTR_retriever is a highly accurate and sensitive program for identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also…
  ☆215Updated 7 months ago
• tangerzhang / ALLHiC
  ALLHiC: phasing and scaffolding polyploid genomes based on Hi-C data
  ☆177Updated last year
• voichek / kmersGWAS
  A library for running k-mers based GWAS
  ☆125Updated last year
• simonhmartin / genomics_general
  General tools for genomic analyses.
  ☆385Updated 11 months ago
• roblanf / minion_qc
  Quality control for MinION sequencing data
  ☆216Updated 3 years ago
• millanek / Dsuite
  Fast calculation of Patterson's D (ABBA-BABA) and the f4-ratio statistics across many populations/species
  ☆183Updated last year
• a-slide / pycoQC
  pycoQC computes metrics and generates Interactive QC plots from the sequencing summary report generated by Oxford Nanopore technologies b…
  ☆284Updated last year
• jtlovell / GENESPACE
  ☆232Updated last year
• hahnlab / CAFE
  Analyze changes in gene family size and provide a statistical foundation for evolutionary inferences.
  ☆119Updated 4 years ago
• mahulchak / quickmerge
  A simple and fast metassembler and assembly gap filler designed for long molecule based assemblies.
  ☆207Updated 3 years ago
• schneebergerlab / plotsr
  Tool to plot synteny and structural rearrangements between genomes
  ☆340Updated 10 months ago
• Dfam-consortium / RepeatMasker
  RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.
  ☆290Updated last month
• BGI-shenzhen / PopLDdecay
  PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format(VCF) files
  ☆202Updated last year
• marbl / merqury
  k-mer based assembly evaluation
  ☆338Updated last year
• Nextomics / NextPolish
  Fast and accurately polish the genome generated by long reads.
  ☆240Updated last year
• hewm2008 / NGenomeSyn
  Any Way to Show Multi genomic Synteny
  ☆217Updated 7 months ago
• malonge / RaGOO
  RaGOO is no longer supported. Please use RagTag instead: https://github.com/malonge/RagTag
  ☆173Updated 4 years ago
• oushujun / EDTA
  Extensive de-novo TE Annotator
  ☆428Updated 3 months ago
• sanger-pathogens / snp-sites
  Finds SNP sites from a multi-FASTA alignment file
  ☆273Updated 5 years ago
• linzhi2013 / MitoZ
  MitoZ: A toolkit for assembly, annotation, and visualization of animal mitochondrial genomes
  ☆135Updated last year