Alternatives and similar repositories for psmc

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

• popgenmethods / smcpp
  SMC++ infers population history from whole-genome sequence data.
  ☆167Updated last year
• tpoorten / dotPlotly
  Generate an interactive dot plot from mummer or minimap alignments
  ☆209Updated last year
• BGI-shenzhen / PopLDdecay
  PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format(VCF) files
  ☆199Updated last year
• voichek / kmersGWAS
  A library for running k-mers based GWAS
  ☆116Updated 11 months ago
• millanek / Dsuite
  Fast calculation of Patterson's D (ABBA-BABA) and the f4-ratio statistics across many populations/species
  ☆178Updated 9 months ago
• szpiech / selscan
  Haplotype based scans for selection
  ☆132Updated this week
• ksamuk / pixy
  Software for painlessly estimating average nucleotide diversity within and between populations
  ☆143Updated last month
• jtlovell / GENESPACE
  ☆218Updated 8 months ago
• hahnlab / CAFE
  Analyze changes in gene family size and provide a statistical foundation for evolutionary inferences.
  ☆118Updated 4 years ago
• hardingnj / xpclr
  Code to compute the XP-CLR statistic to infer natural selection
  ☆98Updated 3 years ago
• hahnlab / CAFE5
  Version 5 of the CAFE phylogenetics software
  ☆149Updated 8 months ago
• linzhi2013 / MitoZ
  MitoZ: A toolkit for assembly, annotation, and visualization of animal mitochondrial genomes
  ☆130Updated 11 months ago
• hillerlab / TOGA
  TOGA (Tool to infer Orthologs from Genome Alignments): implements a novel paradigm to infer orthologous genes. TOGA integrates gene annot…
  ☆195Updated 3 months ago
• JimWhiting91 / genotype_plot
  A set of functions to visualise genotypes based on a VCF
  ☆87Updated 3 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…
  ☆210Updated 3 months ago
• chrishah / MITObim
  MITObim - mitochondrial baiting and iterative mapping
  ☆114Updated 4 years ago
• speciationgenomics / scripts
  Scripts for analysis used during the course
  ☆92Updated last year
• malonge / RaGOO
  RaGOO is no longer supported. Please use RagTag instead: https://github.com/malonge/RagTag
  ☆172Updated 4 years ago
• tangerzhang / ALLHiC
  ALLHiC: phasing and scaffolding polyploid genomes based on Hi-C data
  ☆177Updated 11 months ago
• marcelauliano / MitoHiFi
  Find, circularise and annotate mitogenome from PacBio assemblies
  ☆188Updated 5 months ago
• ruanjue / smartdenovo
  Ultra-fast de novo assembler using long noisy reads
  ☆134Updated 4 years ago
• chasewnelson / SNPGenie
  Program for estimating πN/πS, dN/dS, and other diversity measures from next-generation sequencing data
  ☆117Updated 2 years ago
• ANGSD / angsd
  Program for analysing NGS data.
  ☆243Updated 7 months ago
• sanger-pathogens / assembly-stats
  Get assembly statistics from FASTA and FASTQ files
  ☆123Updated 2 years ago
• baoxingsong / AnchorWave
  Sensitive alignment of genomes with high sequence diversity, extensive structural polymorphism and whole-genome duplication variation
  ☆176Updated 5 months ago
• edgardomortiz / vcf2phylip
  Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis
  ☆318Updated 2 years ago
• hewm2008 / NGenomeSyn
  Any Way to Show Multi genomic Synteny
  ☆204Updated 3 months ago
• isaacovercast / easySFS
  Effective selection of population size projection for construction of the site frequency spectrum. Convert VCF to dadi/fastsimcoal style …
  ☆156Updated last year
• tbenavi1 / genomescope2.0
  Reference-free profiling of polyploid genomes
  ☆126Updated last week
• ColonnaLab / EMBO_popgen
  ☆17Updated 3 months ago