| Minimap2: pairwise alignment for nucleotide sequences |
537 |
| ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R |
514 |
| fastp: an ultra-fast all-in-one FASTQ preprocessor |
513 |
| Nextstrain: real-time tracking of pathogen evolution |
193 |
| RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference |
192 |
| VarSome: the human genomic variant search engine |
156 |
| NanoPack: visualizing and processing long-read sequencing data |
146 |
| Benchmarking fold detection by DaliLite v.5 |
107 |
| DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication |
105 |
| Parallelization of MAFFT for large-scale multiple sequence alignments |
100 |
| NGL viewer: web-based molecular graphics for large complexes |
85 |
| FROGS: Find, Rapidly, OTUs with Galaxy Solution |
79 |
| TISIDB: an integrated repository portal for tumor-immune system interactions |
79 |
| MetaboAnalystR: an R package for flexible and reproducible analysis of metabolomics data |
77 |
| iFeature: a Python package and web server for features extraction and selection from protein and peptide sequences |
76 |
| Predicting miRNA-disease association based on inductive matrix completion |
76 |
| Updating the 97% identity threshold for 16S ribosomal RNA OTUs |
70 |
| Heavy-tailed prior distributions for sequence count data: removing the noise and preserving large differences |
69 |
| Modeling polypharmacy side effects with graph convolutional networks |
68 |
| PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format files |
68 |
| iTerm-PseKNC: a sequence-based tool for predicting bacterial transcriptional terminators |
68 |
| admetSAR 2.0: web-service for prediction and optimization of chemical ADMET properties |
62 |
| Versatile genome assembly evaluation with QUAST-LG |
60 |
| Identify origin of replication in Saccharomyces cerevisiae using two-step feature selection technique |
57 |
| i6mA-Pred: identifying DNA N-6 - methyladenine sites in the rice genome |
57 |
| DincRNA: a comprehensive web-based bioinformatics toolkit for exploring disease associations and ncRNA function |
57 |
| The lncLocator: a subcellular localization predictor for long non-coding RNAs based on a stacked ensemble classifier |
56 |
| ACPred-FL: a sequence-based predictor using effective feature representation to improve the prediction of anti-cancer peptides |
51 |
| Phandango: an interactive viewer for bacterial population genomics |
50 |
| deepDR: a network-based deep learning approach to in silico drug repositioning |
49 |
| heatmaply: an R package for creating interactive cluster heatmaps for online publishing |
48 |
| BNPMDA: Bipartite Network Projection for MiRNA-Disease Association prediction |
47 |
| IRscope: an online program to visualize the junction sites of chloroplast genomes |
46 |
| iLoc-lncRNA: predict the subcellular location of lncRNAs by incorporating octamer composition into general PseKNC |
45 |
| PhenoScanner V2: an expanded tool for searching human genotype-phenotype associations |
44 |
| DeepDTA: deep drug-target binding affinity prediction |
43 |
| Tumor origin detection with tissue-specific miRNA and DNA methylation markers |
43 |
| Efficient comparative phylogenetics on large trees |
42 |
| The revival of the Gini importance ? |
41 |
| Scaling read aligners to hundreds of threads on general-purpose processors |
41 |
| FATHMM-XF: accurate prediction of pathogenic point mutations via extended features |
41 |
| iPromoter-2L: a two-layer predictor for identifying promoters and their types by multi-window-based PseKNC |
40 |
| SPRING: a kinetic interface for visualizing high dimensional single-cell expression data |
40 |
| Comprehensive evaluation of transcriptome-based cell-type quantification methods for immuno-oncology |
40 |
| GSCALite: a web server for gene set cancer analysis |
39 |
| ARGs-OAP v2.0 with an expanded SARG database and Hidden Markov Models for enhancement characterization and quantification of antibiotic resistance genes in environmental metagenomes |
39 |
| Mosdepth: quick coverage calculation for genomes and exomes |
38 |
| DIABLO: an integrative approach for identifying key molecular drivers from multi-omics assays |
36 |
| A graph regularized non-negative matrix factorization method for identifying microRNA-disease associations |
36 |
| SEED 2: a user-friendly platform for amplicon high-throughput sequencing data analyses |
36 |
