Alternatives and similar repositories for CAFE

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

• hahnlab / CAFE5
  Version 5 of the CAFE phylogenetics software
  ☆158Updated 10 months ago
• chasewnelson / SNPGenie
  Program for estimating πN/πS, dN/dS, and other diversity measures from next-generation sequencing data
  ☆120Updated 2 years ago
• tpoorten / dotPlotly
  Generate an interactive dot plot from mummer or minimap alignments
  ☆210Updated last year
• voichek / kmersGWAS
  A library for running k-mers based GWAS
  ☆123Updated last year
• linzhi2013 / MitoZ
  MitoZ: A toolkit for assembly, annotation, and visualization of animal mitochondrial genomes
  ☆133Updated last year
• baoxingsong / AnchorWave
  Sensitive alignment of genomes with high sequence diversity, extensive structural polymorphism and whole-genome duplication variation
  ☆183Updated 2 months ago
• tangerzhang / ALLHiC
  ALLHiC: phasing and scaffolding polyploid genomes based on Hi-C data
  ☆178Updated last year
• huangnengCSU / compleasm
  A genome completeness evaluation tool based on miniprot
  ☆230Updated 3 months ago
• jtlovell / GENESPACE
  ☆228Updated 11 months ago
• RemiAllio / MitoFinder
  MitoFinder: efficient automated large-scale extraction of mitogenomic data from high throughput sequencing data
  ☆111Updated 3 months ago
• EVidenceModeler / EVidenceModeler
  source code for EVM
  ☆119Updated last year
• sanger-pathogens / assembly-stats
  Get assembly statistics from FASTA and FASTQ files
  ☆124Updated 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…
  ☆216Updated 6 months ago
• xiaochuanle / NECAT
  Nanopore data assembler
  ☆162Updated 3 years ago
• lh3 / psmc
  Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model
  ☆181Updated last month
• hewm2008 / NGenomeSyn
  Any Way to Show Multi genomic Synteny
  ☆215Updated 5 months ago
• zhangrengang / TEsorter
  TEsorter: an accurate and fast method to classify LTR-retrotransposons in plant genomes
  ☆101Updated last month
• qiao-xin / DupGen_finder
  A pipeline used to identify different modes of duplicated gene pairs
  ☆116Updated 5 months ago
• thlee / SNPhylo
  A pipeline to generate a phylogenetic tree from huge SNP data
  ☆93Updated 2 years ago
• DRL / blobtools
  Modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets
  ☆208Updated last year
• malonge / RaGOO
  RaGOO is no longer supported. Please use RagTag instead: https://github.com/malonge/RagTag
  ☆174Updated 4 years ago
• marcelauliano / MitoHiFi
  Find, circularise and annotate mitogenome from PacBio assemblies
  ☆189Updated 7 months ago
• BGI-Qingdao / TGS-GapCloser
  A gap-closing software tool that uses long reads to enhance genome assembly.
  ☆226Updated last year
• eead-csic-compbio / get_homologues
  GET_HOMOLOGUES: a versatile software package for pan-genome analysis
  ☆122Updated last week
• popgenmethods / smcpp
  SMC++ infers population history from whole-genome sequence data.
  ☆169Updated last year
• ncbi / fcs
  Foreign Contamination Screening caller scripts and documentation
  ☆153Updated 9 months ago
• SunPengChuan / wgdi
  WGDI: A user-friendly toolkit for evolutionary analyses of whole-genome duplications and ancestral karyotypes
  ☆153Updated last month
• tbenavi1 / genomescope2.0
  Reference-free profiling of polyploid genomes
  ☆137Updated 2 months ago
• ncbi / egapx
  Eukaryotic Genome Annotation Pipeline-External caller scripts and documentation
  ☆172Updated 2 weeks ago
• ndierckx / NOVOPlasty
  NOVOPlasty - The organelle assembler and heteroplasmy caller
  ☆193Updated last year