Package Programs List (Basic Biology)
Applications available via module
The configuration file must be loaded in advance:
source /apl/bio/etc/bio.sh| Analysis Type | Application | Description | Version | Date | Official URL |
|---|---|---|---|---|---|
| Homology search | blast+ | Sequence Similarity Search | 2.13.0 | 2023/09/11 | link |
| 2.16.0 | 2024/06/26 | ||||
| 2.17.0 | 2026/02/10 | ||||
| blat | BLAT on DNA is designed to quickly find sequences of 95% and greater similarity of length 25 bases or more | 37 | 2023/09/11 | link | |
| 38 | 2025/06/25 | ||||
| cd-hit | CD-HIT is a widely used program for clustering biological sequences to reduce sequence redundancy and improve the performance of other sequence analyses. | 4.8.1 | 2023/09/11 | link | |
| Diamond | DIAMOND is a sequence aligner for protein and translated DNA searches, designed for high performance analysis of big sequence data. | 2.0.15 | 2023/09/11 | link | |
| 2.1.11 | 2025/04/30 | ||||
| 2.1.14 | 2025/09/29 | ||||
| 2.1.16 | 2025/11/20 | ||||
| 2.1.22 | 2026/02/10 | ||||
| fasta | Sequence Similarity Search | 36.3.8g | 2023/09/11 | link | |
| HH-suite | The HH-suite is an open-source software package for sensitive protein sequence searching based on the pairwise alignment of hidden Markov models (HMMs). | 3.3.0_SSE2 | 2023/09/11 | link | |
| MMseq2 | ultra fast and sensitive sequence search and clustering suite | 14-7e284 | 2023/09/11 | link | |
| 17-b804f | 2025/01/18 | ||||
18-8cc5c | 2025/07/27 | ||||
| vsearch | VSEARCH is an open source and free of charge multithreaded 64-bit tool for processing metagenomic nucleotide sequence data. An alternative to the USEARCH | 2.22.1 | 2023/09/11 | link | |
| 2.29.0 | 2024/09/28 | ||||
| NGS analysis | bamtools | Bamtools is a toolkit for analyzing and managing BAM files | 2.5.2 | 2023/09/11 | link |
| bedops | BEDOPS: the fast, highly scalable and easily-parallelizable genome analysis toolkit | 2.4.41 | 2025/03/25 | link | |
| BEDtools | Bedtools utilities are a tools for a wide-range of genomics analysis tasks | 2.27.1 | 2023/09/11 | link | |
| 2.31.1 | 2023/11/08 | ||||
| Bowtie | Bowtie is an ultrafast, memory-efficient short read aligner | 1.2.3 | 2023/09/11 | link | |
| Bowtie2 | Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. | 2.5.1 | 2023/09/11 | link | |
| 2.5.3 | 2024/01/17 | ||||
| bwa | Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence | 0.7.15 | 2023/09/11 | link | |
| 0.7.17 | 2018/05/14 | ||||
| 0.7.19 | 2025/07/17 | ||||
| bwa-mem2 | Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence | 2.2.1 | 2023/09/11 | link | |
| 2.2.3 | 2025/06/30 | ||||
| cutadapt | Cutadapt removes adapter sequences from high-throughput sequencing reads. | 4.9 | 2023/09/11 | link | |
| Cufflinks | Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples | 2.2.1 | 2023/09/11 | link | |
| fastp | A quality control tool for high throughput sequence data. | 0.23.2 | 2023/09/11 | link | |
| 0.23.4 | 2023/10/25 | ||||
| 1.0.1 | 2025/11/20 | ||||
| FastQC | A quality control tool for high throughput sequence data. | 0.12.1 | 2023/03/02 | link | |
| gffcompare | GffCompare provides classification and reference annotation mapping and matching statistics for RNA-Seq assemblies (transfrags) or other generic GFF/GTF files. | 0.12.6 | 2023/09/11 | link | |
| gffread | Filter, convert or cluster GFF/GTF/BED records, extract the sequence of transcripts (exon or CDS) and more. | 0.12.7 | 2023/09/11 | link | |
| hisat2 | HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA). | 2.2.1 | 2025/06/24 | link | |
| jellyfish | Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. | 2.3.0 | 2023/09/11 | link | |
| 2.3.1 | 2024/04/05 | ||||
| kallisto | kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. | 0.46.2 | 2023/09/11 | ||
| 0.51.1 | 2026/02/10 | link | |||
| RSEM | RNA-Seq by Expectation-Maximization | 1.3.3 | 2025/09/15 | link | |
| Salmon | Salmon is a tool for quantifying the expression of transcripts using RNA-seq data | 1.8.0 | 2023/09/11 | link | |
| 1.10.0 | 2023/02/25 | ||||
| 1.10.1 | 2023/03/12 | ||||
| samtools | SAM Tools provide various utilities for manipulating alignments in the SAM format | 1.18 | 2023/09/20 | link | |
| 1.19.2 | 2024/04/05 | ||||
| 1.21 | 2024/11/05 | ||||
| seqkit | SeqKit - a cross-platform and ultrafast toolkit for FASTA/Q file manipulation | 2.3.0 | 2023/09/11 | link | |
| 2.10.0 | 2025/03/25 | ||||
| 2.11.0 | 2026/02/10 | ||||
| SOAP | Short Oligonucleotide Analysis Package | 2.21 | 2018/05/17 | link | |
| SOAPdenovo | Short Oligonucleotide Analysis Package | 2.04 | 2023/09/11 | link | |
| SRAtoolkit | The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives. | 3.0.0 | 2023/09/11 | link | |
| STAR | Spliced Transcripts Alignment to a Reference | 2.7.9a | 2023/09/11 | link | |
| 2.7.11b | 2024/11/05 | ||||
| Stringtie | StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. | 2.2.1 | 2023/09/11 | link | |
| 2.2.3 | 2024/05/08 | ||||
| 3.0.0 | 2025/01/07 | ||||
| Tophat | TopHat is a fast splice junction mapper for RNA-Seq reads | 2.1.1 | 2023/09/11 | link | |
| Metagenome analysis | CAT_pack | A pipelines for the taxonomic classification of long DNA sequences and metagenome assembled genomes (MAGs / bins) | 6.0.1 | 2024/03/12 | link |
| Genome (transcript) Assembler | ABySS | Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler | 2.3.4 | 2023/09/11 | link |
| Allpaths-LG | The new short read genome assembler. | 52415 | 2023/09/11 | link | |
| 52488 | 2023/09/12 | ||||
| canu | Canu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing (such as the PacBio RSII or Oxford Nanopore MinION). | 2.2 | 2023/09/11 | link | |
| Flye | Flye is a de novo assembler for single-molecule sequencing reads. | 2.9.6 | 2026/02/12 | link | |
| hifiasm | Hifiasm is a fast haplotype-resolved de novo assembler for PacBio HiFi reads. | 0.18.5 | 2023/09/11 | link | |
| MaSuRCA | MaSuRCA (Maryland Super-Read Celera Assembler) genome assembly software | 4.0.7 | 2023/09/11 | link | |
| NECAT | NECAT is an error correction and de-novo assembly tool for Nanopore long noisy reads. | 0.0.1 | 2023/09/11 | link | |
| SPAdes | SPAdes St. Petersburg genome assembler: SPAdes is an assembly toolkit containing various assembly pipelines. | 3.15.3 | 2023/09/11 | link | |
| 4.1.0 | 2025/04/30 | ||||
| 4.2.0 | 2025/11/20 | ||||
| Trinityrnaseq | Novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data | 2.15.1 | 2023/09/11 | link | |
| 2.15.2 | 2025/02/12 | ||||
| velvet | Sequence assembler for very short reads | 1.2.10 | 2023/09/11 | link | |
| wgs | same as Celera Assembler: Whole genome assembler | 8.2 | 2023/09/11 | link | |
| Pairwise Alignment | lastz | A tool for (1) aligning two DNA sequences, and (2) inferring appropriate scoring parameters automatically | 1.04 | 2018/05/15 | link |
| MUMmer | MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form. | 3.23 | 2026/02/26 | link | |
| 4.0.1 | 2026/02/12 | ||||
| Multiple Alignment | clustal Omega | Fast, accurate, scalable multiple sequence alignment for proteins | 1.2.4 | 2024/12/05 | link |
| clustalw | Multiple Sequence Alignment | 1.83 | 2023/09/11 | link | |
| clustalw2 | Multiple Sequence Alignment | 2.1 | 2023/09/11 | link | |
| FAMSA | Progressive algorithm for large-scale multiple sequence alignments. | 1.6.2 | 2023/09/11 | link | |
| 2.4.1 | 2025/08/01 | ||||
| Gblocks | Gblocks eliminates poorly aligned positions and divergent regions of an alignment of DNA or protein sequences | 0.91b | 2023/09/11 | linkl | |
| MAFFT | MAFFT is a multiple sequence alignment program | 7.526 | 2025/04/28 | link | |
| muscle | Multiple Sequence Alignment faster and more accurate than clustalw | 5.1 | 2023/09/11 | link | |
| t_coffee | Multiple sequence alignment package | 12.00.7 | 2023/09/11 | link | |
| Genome Aligner | minimap2 | A versatile sequence alignment program that aligns DNA or mRNA sequences against a large reference database | 2-2.30 | 2023/04/26 | link |
| miniprot | Miniprot aligns a protein sequence against a genome with affine gap penalty, splicing and frameshift | 0.18 | 2025/03/08 | link | |
| Database search | dbget | DBGET is an integrated database retrieval system for major biological databases | 6.5 | 2024/12/26 | link |
| Sequence Assembler | CAP3 | CAP3 is a DNA sequence assembly program | 122107 | 2023/09/11 | link |
| consed | Assembly Editor | 29.0 | 2023/09/11 | link | |
| Phrap | Phrap is a program for assembling shotgun DNA sequence data | 1.090518 | 2023/09/11 | link | |
| TGICL | TIGR Gene Indices Clustering tools for clustering and assembling large EST datasets | 2.1 | 2023/09/11 | it's gone | |
| Gene prediction | Augustus | AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences | 3.5.0 | 2023/09/11 | link |
| Genemark | A family of gene prediction programs | 4.69 | 2022/02/10 | link | |
| genscan | Gene prediction | 2003/12/17 | link | ||
| glimmer | Glimmer is a system for finding genes in microbial DNA | 30.02 | 2023/09/11 | link | |
| glimmerhmm | GlimmerHMM is a gene finder based on a Generalized Hidden Markov Model (GHMM) for eukaryotic genomes. | 3.0.4 | 2023/09/11 | link | |
| Metaeuk | MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics | 6-a5d39d9 | 2023/09/11 | link | |
| 7-bba0d80 | 2024/05/30 | ||||
| Prodigal | Prodigal: Fast, reliable protein-coding gene prediction for prokaryotic genomes. | 2.6.3 | 2025/04/30 | link | |
| TSEBRA | TSEBRA is a combiner tool that selects transcripts from gene predictions based on the support by extrisic evidence in form of introns and start/stop codons | 1.1.1 | 2023/09/11 | link | |
| Motif search | HMMER | Biosequence analysis using profile HMM | 3.2.1 | 2018/06/18 | link |
| 3.3.2 | 2023/09/11 | ||||
| 3.4 | 2024/10/03 | ||||
| Interproscan | A tool that combines different protein signature recognition methods into one resource | 5.75-106.0 | 2025/10/06 | link | |
| meme | Multiple Em for Motif Elicitation | 5.4.1 | 2023/09/11 | link | |
| Functional annotation | bakta | Bakta is a tool for the rapid & standardized annotation of bacterial genomes and plasmids from both isolates and MAGs. | 1.12 | 2026/02/13 | link |
| eggNOG-Mapper | A tool for fast functional annotation of novel sequences. | 2.1.12 | 2025/03/04 | link | |
| phylogenetic tree analysis | mrbayes | MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models | 3.2.7 | 2019/03/04 | link |
| 3.2.7.mpi | 2023/09/11 | ||||
| njplot | NJplot is a tree drawing program | 2.4 | 2023/09/11 | link | |
| paup | Tools for inferring and interpreting phylogenetic trees | 4b10 | 2023/09/11 | link | |
| Phylip | A package of programs for inferring phylogenies (evolutionary trees) | 3.695 | 2023/09/11 | link | |
| 3.697 | 2018/05/15 | ||||
| PhyML | PhyML is a phylogeny software based on the maximum-likelihood principle | 3.3 | 2018/05/15 | link | |
| RAxML (raxmlHPC) | RAxML - Randomized Axelerated Maximum Likelihood | 8.2.13 | 2024/11/13 | link | |
| tree-puzzle | Program to reconstruct phylogenetic trees from molecular sequence data by maximum likelihood | 5.2 | 2023/09/11 | link | |
| 5.3.rc16 | 2018/05/15 | ||||
| Single cell analysis | CellRanger | A set of analysis pipelines that perform sample demultiplexing, barcode processing, single cell 3' and 5' gene counting, V(D)J transcript sequence assembly and annotation, and Feature Barcode analysis from single cell data. | 7.1.0 | 2022/11/30 | link |
| 7.2.0 | 2023/09/01 | ||||
| 8.0.1 | 2024/06/18 | ||||
| Repeat Masking | RepeatMasker | RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences | 4.1.2 | 2022/11/04 | link |
| 4.1.3 | 2025/05/01 | ||||
| 4.1.4 | 2022/11/28 | ||||
| 4.1.8 | 2025/05/01 | ||||
| 4.1.9 | 2025/05/06 | ||||
| 4.2.3 | 2026/02/18 | ||||
| RepeatModeler | RepeatModeler is a de novo transposable element (TE) family identification and modeling package. | 2.0.3 | 2022/10/12 | link | |
| 2.0.4 | 2022/12/08 | ||||
| 2.0.6 | 2025/05/26 | ||||
| 2.0.7 | 2026/02/18 | ||||
| tRNA search | tRNAscan-SE | tRNAscan-SE pioneers the large-scale use of covariance models to annotate tRNA genes in genomes | 2.0.12 | 2026/02/12 | link |
| Other | TransDecoder | TransDecoder identifies candidate coding regions within transcript sequences. | 5.5.0 | 2023/09/11 | link |
| 5.7.1 | 2023/07/16 | ||||
| nextflow | Nextflow is a workflow system for creating scalable, portable, and reproducible workflows. | 24.04.2 | 2024/06/21 | link | |
| 25.10.2 | 2025/12/19 | ||||
| Phred | The phred software reads DNA sequencing trace files, calls bases, and assigns a quality value to each called base | 071220 | 2023/09/11 | link | |
| OrthoFinder | OrthoFinder is a fast, accurate and comprehensive platform for comparative genomics. | 3.0.1b1 | 2026/03/13 | link | |
| R | R is a programming language for statistical computing and data visualization. | 4.3.1 | 2024/10/02 | link | |
| 4.4.1 | 2024/10/02 | ||||
| 4.5.1 | 2025/09/10 | ||||
perl | A highly capable, feature-rich programming language widely used in bioinformatics for text processing and scripting. | 5.38.2 | 2024/09/11 | ||
| 5.40.0 | 2024/09/11 | ||||
| 5.40.1 | 2025/01/23 | ||||
| ruby | A dynamic, open source programming language with a focus on simplicity and productivity. | 3.0.1 | 2023/09/11 | ||
| 3.4.4 | 2025/06/25 | ||||
| python3 | A powerful, high-level programming language widely adopted in bioinformatics and data analysis. | 3.7.16 | 2024/06/28 | ||
| 3.8.10 | 2024/09/04 | ||||
| 3.12.4 | 2026/02/12 | ||||
| pyenv | A simple and straightforward tool for managing and switching between multiple Python versions. | 2.6.17 | 2021/10/27 | ||
| sqlite3 | A C-language library that implements a small, fast, self-contained, and high-reliability SQL database engine. | 3.39.2 | 2023/09/11 | ||
| jdk | The Java Development Kit (JDK) is a software development environment used for developing and running Java applications. | 11 | 2019/10/10 | ||
| 11.0.2 | 2019/10/10 | ||||
| 13 | 2019/12/24 | ||||
| 17.0.6 | 2023/3/7 | ||||
| 19.0.2 | 2023/3/7 | ||||
| 24 | 2025/4/2 |
Applications installed as Python 3 modules
- These can be used by loading Python 3 via the module command:
module load python3| Other | MACS3 | Model-based Analysis of ChIP-Seq on short reads sequencers such as Genome Analyzer (Illumina / Solexa) This program was installed using pip. To use it, run `module load python3`. | 3.0.2 | 2025/02/01 | link |
| HTSeq | High-throughput sequence analysis in Python | 2.0.9 | 2024/09/12 | link |
Container .sif files provided for use with Apptainer
- Please use them by creating a symbolic link in your working directory.
- The .sif files are located in the following directory path:
/apl/bio/container/| Application | Description | Version | .sif file | remarks | Date | Official URL |
| AGAT | AGAT has the power to check, fix, pad missing information (features/attributes) of any kind of GTF and GFF to create complete, sorted and standardised gff3 format. | 1.0.0 | AGAT/1.0.0/agat100.sif | 2023-04-12 | link | |
1.4.1 | AGAT/1.4.1/agat_1.4.1--pl5321hdfd78af_0.sif | 2024/11/13 | ||||
| Augustus | AUGUSTUS is a program to find genes and their structures in one or more genomes. | 3.5.0 | Augustus/3.5.0/augustus350.sif | 2026/07/17 | link | |
| BRAKER | BRAKER is a program that predicts genes in eukaryotic genomic sequences | 3.0.2 | BRAKER/3.0.2/braker3.sif | 2023-03-06 | link | |
| 3.0.8 | BRAKER/3.0.8/braker308.sif | 2026-03-03 | ||||
| 3.1.1 | BRAKER/3.1.1/braker311.sif | 2026-07-09 | ||||
| BUSCO | Assessing genome assembly and annotation completeness with single-copy orthologs | 5.8.0 | BUSCO/5.8.0/busco580.sif | Required Options : --offline | 2025-05-13 | link |
| 6.0.0_cv1 | BUSCO/6.0.0_cv1/busco600.sif | 2026-02-13 | ||||
| 6.1.0_cv2 | BUSCO/6.1.0_cv2/busco610.sif | 2026/07/17 | ||||
| DeepConsensus | DeepConsensus uses gap-aware sequence transformers to correct errors in Pacific Biosciences (PacBio) Circular Consensus Sequencing (CCS) data. | 1.2.0 | DeepConsensus/1.2.0/deepconsensus.sif | 2025/05/13 | link | |
| DeepTMHMM | DeepTMHMM is currently the most complete and best-performing method for the prediction of the topology of both alpha-helical and beta-barrel transmembrane proteins. | 1.0.42 | DeepTMHMM/1.0.42/deeptmhmm_edit_g.sif | 2025/05/13 | link | |
| EpiTyping | EpiTyping is a tool for detecting imprinting and X-chromosome inactivation status from RNA-seq | 1 | EpiTyping/epityping.sif | 2025/01/29 | link | |
| GALBA | GALBA uses the protein sequences of several (few) or one closely related species to generate a training gene set for AUGUSTUS with either miniprot or GenomeThreader. | 1.0.7 | GALBA/1.0.7/galba107_aug35.sif | with Augustus 3.5.0 | 2024/11/13 | link |
| GALBA2 | GALBA2 — protein homology based genome annotation in Snakemake | 0.5.0 | GALBA2/0.5.0/galba2-tools.sif | 2026/07/17 | link | |
| GATK | The GATK is the industry standard for identifying SNPs and indels in germline DNA and RNAseq data. | 4.0.1 | GATK/4.0.1/gatk-4.sif | 2025-05-13 | link | |
| 4.6.0 | GATK/4.6.0/gatk-460.sif | 2025-11-18 | ||||
| 4.6.2 | GATK/4.6.2/gatk-426.sif | 2025/11/18 | ||||
| ipyrad | An interactive assembly and analysis toolkit for restriction-site associated DNA (RAD-seq) and related data types. | 0.9.81 | ipyrad/0.9.81/ipyrad_0.9.81--pyh5e36f6f_0 | 2021/06/22 | link | |
| PASA Pipeline | PASA, acronym for Program to Assemble Spliced Alignments (and pronounced 'pass-uh'), is a eukaryotic genome annotation tool that exploits spliced alignments of expressed transcript sequences to automatically model gene structures | 2.5.3 | PASA/2.5.3/pasapipeline.v2.5.3.simg | 2023/06/01 | link |