| Package Name | Access | Summary | Updated |
|---|---|---|---|
| snpeff | public | Genetic variant annotation and effect prediction toolbox | 2025-09-23 |
| snpsift | public | Toolbox that allows you to filter and manipulate annotated files | 2025-09-23 |
| funannotate | public | funannotate: eukaryotic genome annotation pipeline | 2025-09-23 |
| discosnp | public | reference-free small variant caller for short read sequencing data | 2025-09-23 |
| cactus | public | Cactus is a reference-free whole-genome multiple alignment program based upon notion of Cactus graphs | 2025-09-23 |
| assembly-stats | public | Get assembly statistics from FASTA and FASTQ files | 2025-09-23 |
| treebest | public | TreeBeST: Tree Building guided by Species Tree, used in the Ensembl Compara pipeline. | 2025-09-23 |
| samtools | public | Tools for dealing with SAM, BAM and CRAM files | 2025-09-23 |
| mindthegap | public | MindTheGap performs detection and assembly of DNA insertion variants in NGS read datasets with respect to a reference genome. MindTheGap can also be used as a genome assembly finishing tool, it can fill the gaps between a set of input contigs without any a priori on their relative order and orientation. | 2025-09-23 |
| short-read-connector | public | Short read connector enables the comparisons of two read sets | 2025-09-23 |
| upimapi | public | UniProt Id Mapping through API | 2025-09-23 |
| fastuniq | public | No Summary | 2025-09-23 |
| dsk | public | DSK is a k-mer counter for reads or genomes. | 2025-09-22 |
| generax | public | GeneRax: a parallel tool for species tree-aware maximum likelihood based gene tree inference under gene duplication, transfer, and loss. | 2025-09-22 |
| physher | public | A multi-algorithmic framework for phylogenetic inference | 2025-09-22 |
| r-stitch | public | STITCH - Sequencing To Imputation Through Constructing Haplotypes. | 2025-09-22 |
| b2btools | public | The bio2Byte software suite to predict protein biophysical properties | 2025-09-22 |
| fasta3 | public | The FASTA package - protein and DNA sequence similarity searching and alignment programs | 2025-09-22 |
| savana | public | SAVANA: a somatic structural variant caller for long-read data. | 2025-09-22 |
| knotinframe | public | Predicts -1 frameshift sites with simple pseudoknots | 2025-09-22 |
| glimmerhmm | public | No Summary | 2025-09-22 |
| ipk | public | IPK is a tool for computing phylo-k-mers for a fixed phylogeny. | 2025-09-22 |
| relion | public | Image-processing software for cryo-electron microscopy. | 2025-09-22 |
| excludonfinder | public | A tool for identifying and analyzing excludons in genomic data using RNA-seq data. | 2025-09-22 |
| visceral-evaluatesegmentation | public | EvaluateSegmentation is a tool that compares two volumes (a test segmentation and a ground truth segmentation) using 22 different metrics that were selected as a result of a comprehensive research into the metrics used in the medical volume segmentations. | 2025-09-22 |
