Alternatives and similar repositories for CAFE5:

Users that are interested in CAFE5 are comparing it to the libraries listed below

• hahnlab / CAFE
  Analyze changes in gene family size and provide a statistical foundation for evolutionary inferences.
  ☆115Updated 3 years ago
• linzhi2013 / MitoZ
  MitoZ: A toolkit for assembly, annotation, and visualization of animal mitochondrial genomes
  ☆119Updated 2 months ago
• tpoorten / dotPlotly
  Generate an interactive dot plot from mummer or minimap alignments
  ☆194Updated last year
• zhangrengang / TEsorter
  TEsorter: an accurate and fast method to classify LTR-retrotransposons in plant genomes
  ☆90Updated 3 weeks ago
• jtlovell / GENESPACE
  ☆196Updated 5 months ago
• chenlianfu / geta
  ☆73Updated 6 months ago
• sanger-pathogens / assembly-stats
  Get assembly statistics from FASTA and FASTQ files
  ☆116Updated last year
• qiao-xin / DupGen_finder
  A pipeline used to identify different modes of duplicated gene pairs
  ☆94Updated 4 years ago
• hewm2008 / NGenomeSyn
  Any Way to Show Multi genomic Synteny
  ☆166Updated 2 months ago
• TobyBaril / EarlGrey
  Earl Grey: A fully automated TE curation and annotation pipeline
  ☆152Updated this week
• 4ureliek / Parsing-RepeatMasker-Outputs
  Few scripts facilitating the extraction of info from Repeat Masker .out files
  ☆78Updated 3 years ago
• millanek / Dsuite
  Fast calculation of Patterson's D (ABBA-BABA) and the f4-ratio statistics across many populations/species
  ☆166Updated 3 weeks ago
• huangnengCSU / compleasm
  A genome completeness evaluation tool based on miniprot
  ☆188Updated 3 months ago
• tbenavi1 / genomescope2.0
  Reference-free profiling of polyploid genomes
  ☆111Updated 6 months ago
• chasewnelson / SNPGenie
  Program for estimating πN/πS, dN/dS, and other diversity measures from next-generation sequencing data
  ☆110Updated last year
• jamiemcg / BUSCO_phylogenomics
  BUSCO Phylogenomics | Utility script to construct species phylogenies using BUSCO proteins
  ☆58Updated 3 months ago
• steuernb / NLR-Annotator
  NLR-Annotator upload
  ☆62Updated last year
• conchoecia / odp
  oxford dot plots
  ☆142Updated last week
• RemiAllio / MitoFinder
  MitoFinder: efficient automated large-scale extraction of mitogenomic data from high throughput sequencing data
  ☆93Updated 9 months ago
• xiaochuanle / NECAT
  Nanopore data assembler
  ☆140Updated 2 years ago
• MetazoaPhylogenomicsLab / FANTASIA
  ☆26Updated last month
• Nextomics / NextPolish
  Fast and accurately polish the genome generated by long reads.
  ☆215Updated last week
• LKremer / CAFE_fig
  A tool to extract and visualize the results of CAFE (Computational Analysis of gene Family Evolution)
  ☆61Updated 5 years ago
• c-zhou / yahs
  Yet another Hi-C scaffolding tool
  ☆136Updated 2 months ago
• tangerzhang / ALLHiC
  ALLHiC: phasing and scaffolding polyploid genomes based on Hi-C data
  ☆175Updated 2 months ago
• ncbi / egapx
  Eukaryotic Genome Annotation Pipeline-External caller scripts and documentation
  ☆106Updated last week
• marcelauliano / MitoHiFi
  Find, circularise and annotate mitogenome from PacBio assemblies
  ☆171Updated this week
• moiexpositoalonsolab / grenepipe
  A flexible, scalable, and reproducible pipeline to automate variant calling from raw sequence reads, with lots of bells and whistles.
  ☆95Updated last month
• DyogenIBENS / Agora
  Algorithm For Gene Order Reconstruction in Ancestors
  ☆72Updated 2 months ago
• quxiaojian / PGA
  Plastid Genome Annotator
  ☆49Updated 4 years ago