ArticleNucleic acids research2017
CAFE: aCcelerated Alignment-FrEe sequence analysis.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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Who cites it
41 citing papers in PubMed.
- Near telomere-to-telomere genome assembly enables the discovery of introgressed purple-leaf geneHorticulture research · 2026Article
- CAKR: commutative algebra k-mer representations for genomics.Nature communications · 2026Article
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- Insights into karyotype evolution and flower color variation from the genome assembly of wallflower (Erysimum cheiri).Plant physiology · 2026Article
- Telomere-to-telomere genome assembly of a male pig provides insight into population structure and selection for body stature.Nature genetics · 2026Article
- Machine Learning Enables Alignment-Free Distance Calculation and Phylogenetic Placement Using k-Mer Frequencies.Molecular ecology resources · 2025Article
- Chromosome-level genome assembly of Turpan wonder gecko (Teratoscincus roborowskii) reveals olfactory candidate genes.Scientific data · 2025Article
- An alignment-free method for phylogeny estimation using maximum likelihood.BMC bioinformatics · 2025Article
- Reconstruction of masked sequencesPeerJ · 2025Article
- The optimal metric for viral genome space.Computational and structural biotechnology journal · 2024Article
- TreeWave: command line tool for alignment-free phylogeny reconstruction based on graphical representation of DNA sequences and genomic signal processing.BMC bioinformatics · 2024Article
- The genome assembly of Carex breviculmis provides evidence for its phylogenetic localization and environmental adaptation.Annals of botany · 2024Article
- Article
- Chromosome-level genome assembly of Hippophae tibetana provides insights into high-altitude adaptation and flavonoid biosynthesis.BMC biology · 2024Article
- Anomaly Detection Models for SARS-CoV-2 Surveillance Based on GenomeMicroorganisms · 2023Article
- Whole-genome sequencing and evolutionary analysis of the wild edible mushroom,Frontiers in microbiology · 2023Article
- Comparison of k-mer-basedMicrobiome research reports · 2023Article
- Interpreting alignment-free sequence comparison: what makes a score a good score?NAR genomics and bioinformatics · 2022Article
- The Statistics ofJournal of computational biology : a journal of computational molecular cell biology · 2022Article
- Article
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Authors and funding
6 authors.
Funding
Abstract
Alignment-free genome and metagenome comparisons are increasingly important with the development of next generation sequencing (NGS) technologies. Recently developed state-of-the-art k-mer based alignment-free dissimilarity measures including CVTree, $d_2^*$ and $d_2^S$ are more computationally expensive than measures based solely on the k-mer frequencies. Here, we report a standalone software, aCcelerated Alignment-FrEe sequence analysis (CAFE), for efficient calculation of 28 alignment-free dissimilarity measures. CAFE allows for both assembled genome sequences and unassembled NGS shotgun reads as input, and wraps the output in a standard PHYLIP format. In downstream analyses, CAFE can also be used to visualize the pairwise dissimilarity measures, including dendrograms, heatmap, principal coordinate analysis and network display. CAFE serves as a general k-mer based alignment-free analysis platform for studying the relationships among genomes and metagenomes, and is freely available at https://github.com/younglululu/CAFE.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.