| Package Name | Access | Summary | Updated |
|---|---|---|---|
| poreplex | public | Signal-level preprocessor for Oxford Nanopore direct RNA sequencing (DRS) data. Poreplex does many preprocessing steps required before the downstream analyses for RNA Biology and yields the processed data in the ready-to-use forms. | 2025-03-25 |
| hyphy | public | An open-source software package for comparative sequence analysis using stochastic evolutionary models. | 2025-03-25 |
| fastx_toolkit | public | The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing. Next-Generation sequencing machines usually produce FASTA or FASTQ files, containing multiple short-reads sequences (possibly with quality information). The main processing of such FASTA/FASTQ files is mapping (aka aligning) the sequences to reference genomes or other databases using specialized programs. Example of such mapping programs are: Blat, SHRiMP, LastZ, MAQ and many many others. However, it is sometimes more productive to preprocess the FASTA/FASTQ files before mapping the sequences to the genome - manipulating the sequences to produce better mapping results. The FASTX-Toolkit tools perform some of these preprocessing tasks. | 2025-03-25 |
| hicpro | public | An intuitive HyPhy interface for Python | 2025-03-25 |
| python-hyphy-python | public | HyPhy package interface library | 2025-03-25 |
| stacks | public | Stacks is a software pipeline for building loci from RAD-seq | 2025-03-25 |
| python-hivclustering | public | A Python 3 library that makes inferences on HIV-1 transmission networks. | 2025-03-25 |
| gcc | public | The GNU Compiler Collection | 2025-03-25 |
| python-bioext | public | A few handy bioinformatics tools not already in BioPython | 2025-03-25 |
| unicycler | public | Hybrid assembly pipeline for bacterial genomes | 2025-03-25 |
