{"id":11061,"date":"2026-01-20T18:45:37","date_gmt":"2026-01-21T02:45:37","guid":{"rendered":"https:\/\/iada.ubd.edu.bn\/?page_id=11061"},"modified":"2026-01-21T17:02:50","modified_gmt":"2026-01-22T01:02:50","slug":"software-list","status":"publish","type":"page","link":"https:\/\/iada.ubd.edu.bn\/?page_id=11061","title":{"rendered":"Software List"},"content":{"rendered":"\n

Engineering<\/h2>\n\n\n\n
Software<\/strong><\/td>Open Source? (or Licensed)<\/strong><\/td>Description<\/strong><\/td><\/tr>
ANSYS (2023-R2)<\/td>No
Other License: Student License<\/td>		Industry-standard multiphysics simulation suite for structural, thermal, and fluid analyses.<\/td><\/tr>
ANSYS Electronics Desktop(2023 [includes ansys HFSS])<\/td>No
Other License: Student License<\/td>		Electromagnetic field simulation platform (HFSS, Maxwell, etc.) used for antenna, RF, and PCB design.<\/td><\/tr>
Comsol Multiphysics (ver. 5.3a)<\/td>No<\/td>Comprehensive finite-element analysis (FEA) and multiphysics modeling software.<\/td><\/tr>
FreeFEM (ver. 4.10)<\/td>Yes<\/td>Open-source partial differential equation (PDE) solver using the finite element method (FEM).<\/td><\/tr>
Gmsh (ver. 4.11)<\/td>Yes<\/td>3D finite element mesh generator with built-in CAD and post-processing tools.<\/td><\/tr>
MathWorks MATLAB (ver. R2018b)<\/td>No
Other License: Student License<\/td>		High-level technical computing language and environment for numerical analysis and data visualization.<\/td><\/tr>
Network-simulator NS-2 (ver. 2.34)<\/td>Yes<\/td>Discrete event network simulator widely used for academic research in network protocols and systems.<\/td><\/tr>
OpenFoam (ver. 2.4, 5.0)<\/td>Yes<\/td>C++ toolbox for computational fluid dynamics (CFD) and continuum mechanics simulations.<\/td><\/tr>
Peridigm (ver. 1.5)<\/td>Yes<\/td>Open-source code for peridynamic solid mechanics modeling (nonlocal fracture and damage simulation).<\/td><\/tr>
SalomeMeca (ver. 2015)<\/td>Yes<\/td>Open-source platform for pre\/post-processing and coupling of numerical solvers (based on SALOME + Code_Aster).<\/td><\/tr>
Scilab (ver. 5.4)<\/td>Yes<\/td>Open-source numerical computation software similar to MATLAB, for mathematics and engineering applications.<\/td><\/tr><\/tbody><\/table><\/figure>\n\n\n\n

Computational Chemistry<\/h2>\n\n\n\n
Software<\/strong><\/td>Open Source? (or Licensed)<\/strong><\/td>Description<\/strong><\/td><\/tr>
CP2K (ver. 6.1)<\/td>Yes<\/td>Quantum chemistry and solid-state simulation package supporting DFT, MD, and hybrid QM\/MM methods.<\/td><\/tr>
Crystal explorer (ver. 21.3)<\/td>Yes<\/td>Tool for visualizing and analyzing intermolecular interactions and crystal packing in molecular crystals.<\/td><\/tr>
CSDS (ver.2022)<\/td>No<\/td>Cambridge Structural Database System \u2014 database and tools for crystallographic structure data analysis.<\/td><\/tr>
Gaussian (ver. g09_d01)<\/td>No<\/td>Widely used ab initio and DFT electronic structure program for molecular systems.<\/td><\/tr>
GROMACS (ver. 2018-2, 2021, 2022.3)<\/td>Yes<\/td>High-performance molecular dynamics (MD) package for biomolecular and materials simulation.<\/td><\/tr>
Gulp (ver.6.0, 6.1.2)<\/td>Yes<\/td>General Utility Lattice Program \u2014 atomistic simulations for solids, surfaces, and defects.<\/td><\/tr>
Jmol (ver.14.30.2)<\/td>Yes<\/td>Open-source Java viewer for chemical structures in 3D, used in research and teaching.<\/td><\/tr>
Mopac (ver.2016)<\/td>Yes<\/td>Semi-empirical quantum chemistry program for molecular orbital calculations.<\/td><\/tr>
NAMD (ver.2.14-multicore-cuda)<\/td>Yes<\/td>Parallel molecular dynamics engine optimized for large biomolecular systems.<\/td><\/tr>
NWChem(ver. 7.0.2-conda)<\/td>Yes<\/td>Open-source computational chemistry package supporting quantum and molecular dynamics methods.<\/td><\/tr>
ORCA (ver.4.2.1, 5.0.1)<\/td>No<\/td>Quantum chemistry software with DFT, MP2, and coupled-cluster methods; widely used in spectroscopy.<\/td><\/tr>
Plumed (ver. 2.5.0, 2.7.2)<\/td>Yes<\/td>Open-source plugin for enhanced sampling, free-energy calculations, and analysis in MD simulations.<\/td><\/tr>
Pycharm(ver. 2020.2.3)<\/td>Free for basic\/ Pro features are paid subscription

Other License: Student License<\/td>		Python IDE (not chemistry software itself, but used for scripting scientific workflows).<\/td><\/tr>
Pymol (ver.  2.3.0, 2.5.0)<\/td>Mixed, Paid subscription license<\/td>Molecular visualization and analysis tool for structural biology and computational chemistry.<\/td><\/tr>
Schrodinger (ver.2018-4, 2022-1, 2022-4, 2023-2)<\/td>No<\/td>Comprehensive molecular modeling, docking, and quantum chemistry software package.<\/td><\/tr>
VMD (ver.1.9.3 )<\/td>Yes<\/td>Visualization and analysis tool for molecular dynamics simulations, often paired with NAMD and GROMACS.<\/td><\/tr><\/tbody><\/table><\/figure>\n\n\n\n

Bioinformatics\/Genomics<\/h2>\n\n\n\n
Software<\/strong><\/td>Open Source? (or Licensed)<\/strong><\/td>Description<\/strong><\/td><\/tr>
Bcftools (ver. 1.10.2)<\/td>Yes<\/td>Utilities for manipulating variant-calls in VCF\/BCF formats (filtering, indexing, merging)<\/td><\/tr>
Bcl2fastq (ver. 1.8.4, 2.20.0)<\/td>Yes<\/td>Tool converting Illumina base-call files (BCL) to FASTQ format<\/td><\/tr>
Bedops (ver. 2.4.39)<\/td>Yes<\/td>High-performance command-line utilities for set operations on genomic interval files<\/td><\/tr>
Bedtools (ver. 2.29.2)<\/td>Yes<\/td>Suite for \u201cgenome arithmetic\u201d: intersecting, merging, subtracting genomic interval files (BED\/VCF etc)<\/td><\/tr>
Bowtie2 (ver. 2.4.1, 2.4.2)<\/td>Yes<\/td>Ultrafast and memory-efficient aligner of sequencing reads (supports gaps, local\/paired-end)<\/td><\/tr>
Bracken (ver. 2.5)<\/td>Yes<\/td>Bayesian re\u2010estimation of species abundances from Kraken-classified reads<\/td><\/tr>
Chopper (ver. 0.3.0)<\/td>Yes<\/td>Long-read quality trimming \/ filtering tool for genome sequencing<\/td><\/tr>
Cutadapt (ver. 3.5)<\/td>Yes<\/td>Tool to remove adapter sequences and perform trimming\/filtering on reads<\/td><\/tr>
DeepVariant (ver. 1.0.0)<\/td>Yes<\/td>Deep-learning based variant caller, uses TensorFlow models for calling SNPs\/indels<\/td><\/tr>
Diamond (ver. 2.0.3)<\/td>Yes<\/td>Fast sequence aligner (protein\/translated search) optimized for large-scale shotgun\/metagenomic data<\/td><\/tr>
Dorado (ver. 0.1.1)<\/td>Yes<\/td>–<\/td><\/tr>
Drop (ver. 1.1.4)<\/mark><\/td>–<\/td>–<\/td><\/tr>
Fastp (ver. 0.21.0)<\/td>Yes<\/td>Ultra-fast all-in-one FASTQ preprocessor: quality filtering, trimming, adapter removal<\/td><\/tr>
Fastqc (ver. 0.11.9)<\/td>Yes<\/td>Quality-control tool for high-throughput sequencing data (FASTQ\/BAM) generating QC reports<\/td><\/tr>
GATK4 (ver. 4.1.8.1)<\/td>Yes<\/td>Toolkit for variant discovery\/processing (SNPs, indels) and sequence-data pre-\/post-processing<\/td><\/tr>
HTseq (ver. 0.11.3)<\/td>Yes<\/td>Python library and tools for processing high-throughput sequencing data (counting, expression analysis)<\/td><\/tr>
HTSlib (ver. 1.11)<\/td>Yes<\/td>C library for reading\/writing high-throughput sequencing alignment formats (SAM\/BAM\/CRAM)<\/td><\/tr>
Humann2 (ver. 2.81)<\/td>Yes<\/td>Pipeline for functional profiling of microbial communities from metagenomic shotgun data (gene families\/pathways)<\/td><\/tr>
Kraken2 (ver. 2.0.9-beta)<\/td>Yes<\/td>Ultra\u2010fast taxonomic classifier for metagenomic reads using k-mer\/LCA methods<\/td><\/tr>
Lofreq (ver. 2.1.5)<\/td>Yes<\/td>Ultra-sensitive variant caller for low-frequency variants in viral\/amplicon sequencing<\/td><\/tr>
Mafft (ver. 7.471)<\/td>Yes<\/td>Multiple sequence alignment tool for nucleotide\/protein sequences \u2014 high speed\/accuracy<\/td><\/tr>
Medaka (ver. 1.7.3)<\/td>Yes<\/td>Consensus & variant calling tool for Oxford Nanopore Technologies long-reads<\/td><\/tr>
Metaphlan2 (ver. 2.6.0, 2.7.7)<\/td>Yes<\/td>Tool for profiling microbial community composition (species\/strain) from metagenomic data<\/td><\/tr>
Metaphlan3 (ver. 3.0.2)<\/td>Yes<\/td>Updated version of MetaPhlAn pipeline for metagenomic profiling<\/td><\/tr>
Metaphlan4 (ver. 4.0.6)<\/td>Yes<\/td>Next-generation of MetaPhlAn suite with updated databases\/algorithms<\/td><\/tr>
Nanofilt (ver. 2.8.0)<\/td>Yes<\/td>Filtering tool for long-read sequencing data (Nanopore\/PacBio) based on quality\/length<\/td><\/tr>
Plink (ver. 1.90b6.21)<\/td>Yes<\/td>Whole-genome association analysis toolset (GWAS, population genetics)<\/td><\/tr>
Raven (ver. 1.8.1)<\/td>Yes<\/td>Genome assembler for long-reads (Nanopore\/PacBio), efficient in time\/memory<\/td><\/tr>
Saige (ver. 0.44.6.5)<\/td>Yes<\/td>Scalable mixed-model association tests for large biobank data (GWAS)<\/td><\/tr>
Samtools (ver. 1.9, 1.10)<\/td>Yes<\/td>Toolkit for processing SAM\/BAM\/CRAM alignment files: sorting, indexing, viewing, variant calling<\/td><\/tr>
SRA Toolkit (ver. 3.0.1)<\/td>Yes<\/td>Toolkit for accessing and retrieving sequencing data from NCBI\u2019s Sequence Read Archive<\/td><\/tr>
STAR (vera2.7.5c)<\/td>Yes<\/td>Spliced-transcript aligner, ultra-fast alignment of RNA-seq reads (splice-aware)<\/td><\/tr>
Strelka2 (ver. 2.9.10)<\/td>Yes<\/td>Small-variant caller (SNPs\/indels) optimized for tumour\/normal and germline workflows<\/td><\/tr>
Trapd<\/td>Yes<\/td>A burden-testing tool for rare variants, designed to compare case variant burdens against publicly-available summary-level control data<\/td><\/tr>
Trimmomatic (ver. 0.39)<\/td>Yes<\/td>Flexible read\u00adtrimming tool for Illumina sequencing: adapters, quality, length filters<\/td><\/tr>
VEP (ver. 101)<\/td>Yes<\/td>Variant Effect Predictor: annotates effects of genomic variants (genes, transcripts, regulatory)<\/td><\/tr>
Varscan (ver. 2.4.4)<\/td>Yes<\/td>Variant caller for low-frequency variants, indels and copy-number in sequencing data<\/td><\/tr>
Vcftools (ver. 0.1.17)<\/td>Yes<\/td>Tools for manipulating and analysing VCF files (filtering, summarising, annotation)<\/td><\/tr>
Vep (ver. 101, 104.3, 108.2)<\/td>Yes<\/td>Variant Effect Predictor: annotates effects of genomic variants (genes, transcripts, regulatory)<\/td><\/tr>
Vsearch (ver. 2.15.0)<\/td>Yes<\/td>Open-source alternative to USEARCH: clustering, dereplication, chimera detection of sequences<\/td><\/tr><\/tbody><\/table><\/figure>\n\n\n\n

Other<\/h2>\n\n\n\n
Software<\/strong><\/td>Open Source? (or Licensed)<\/strong><\/td>Description<\/strong><\/td><\/tr>
Agisoft PhotoScan<\/td>No<\/td>Photogrammetry software for 3D reconstruction from imagery.<\/td><\/tr>
Apptainer (ver. 1.1.6)<\/td>Yes<\/td>A container\/virtualisation runtime focused on reproducibility & HPC usage.<\/td><\/tr>
Blender (ver. 2.7)<\/td>Yes<\/td>Open-source 3D modelling, animation, rendering tool.<\/td><\/tr>
Git (ver. 1.8.3.1. 2.41.0)<\/td>Yes<\/td>Distributed version control system widely used for software development.<\/td><\/tr>
Hashcat<\/td>Yes<\/td>High-performance password recovery \/ hash-cracking tool.<\/td><\/tr>
R (ver. 3.4.0, 3.5.3, 3.6.3,4.1.0)<\/td>Yes<\/td>Free software environment for statistical computing and graphics.<\/td><\/tr>
Singularity (ver. 3.2.1, 3.4.1, 3.11.4)<\/td>Yes<\/td>Containerisation platform designed for HPC \/ reproducible compute environments.<\/td><\/tr><\/tbody><\/table><\/figure>\n\n\n\n

Programming Tools and Compilers<\/h2>\n\n\n\n
Software<\/strong><\/td>Open Source? (or Licensed)<\/strong><\/td>Description<\/strong><\/td><\/tr>
Conda\/Anaconda (ver. 4.7.5, 4.7.10, 4.13.0, 23.1.0)<\/td>Free and Paid version<\/td>Cross-platform package and environment manager (especially for Python\/R), and distribution of scientific packages.<\/td><\/tr>
CUDA Toolkit (ver. 8.0, 9.2, 10.1, 11.4), cuDNN<\/td>Proprietary<\/td>GPU-accelerated development toolkit: libraries, compilers, runtimes for heterogeneous\/parallel computing on NVIDIA GPUs.<\/td><\/tr>
GNU Compiler Collection (ver. 4.8.5, 5.4.0,7.3.0, 8.3.0, 11.2)<\/td>Yes<\/td>The standard free compiler suite for C, C++, Fortran, and other languages \u2014 widely used in open-source and research.<\/td><\/tr>
Intel Parallel Studio (ver. 2015)\/ IntelMPI (ver. 4.0.3)<\/td>Proprietary<\/td>Commercial high-performance development suite with Intel\u2019s compilers, libraries, MPI, threading tools for parallel computing.<\/td><\/tr>
Jaer 1.8.1<\/td>Yes<\/td>Software likely related to event-based vision (Dynamic Vision Sensors) \u2013 used in certain research contexts.<\/td><\/tr>
OpenACC (3.1)<\/td>Yes<\/td>Compiler directive standard for parallel computing targeting GPUs or accelerators (e.g., \u201c#pragma acc\u201d).<\/td><\/tr>
OpenCL (3.0)<\/td>Yes<\/td>Framework for writing programs that execute across heterogeneous platforms (CPUs, GPUs, FPGAs etc).<\/td><\/tr>
OpenCV (4.5)<\/td>Yes<\/td>Open-source computer vision and machine learning library \u2014 real-time image\/video processing across multiple languages\/platforms.<\/td><\/tr>
OpenMPI (ver. 1.10.7, 3.1.1, 4.0.5, 4.1.1)<\/td>Yes<\/td>High-performance Message Passing Interface library for parallel\/distributed computing (clusters, supercomputers).<\/td><\/tr>
Mamba (1.4.4)<\/td>Yes<\/td>Fast drop-in alternative to Conda for package\/environment management, optimized performance for dependency resolution.<\/td><\/tr>
Perl (ver. 5)<\/td>Yes<\/td>High-level scripting language, often used for system-administration, text processing, rapid prototyping.<\/td><\/tr>
Python (ver. 2.7, 3.6)<\/td>Yes<\/td>Widely-used high-level programming language in research, science, engineering, scripting, data-analysis.<\/td><\/tr><\/tbody><\/table><\/figure>\n\n\n\n

<\/p>\n","protected":false},"excerpt":{"rendered":"

Engineering Software Open Source? (or Licensed) Description ANSYS (2023-R2) NoOther License: Student License Industry-standard multiphysics simulation suite for structural, thermal, […]<\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-11061","page","type-page","status-publish","hentry","post"],"_links":{"self":[{"href":"https:\/\/iada.ubd.edu.bn\/index.php?rest_route=\/wp\/v2\/pages\/11061","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/iada.ubd.edu.bn\/index.php?rest_route=\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/iada.ubd.edu.bn\/index.php?rest_route=\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/iada.ubd.edu.bn\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/iada.ubd.edu.bn\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=11061"}],"version-history":[{"count":14,"href":"https:\/\/iada.ubd.edu.bn\/index.php?rest_route=\/wp\/v2\/pages\/11061\/revisions"}],"predecessor-version":[{"id":11100,"href":"https:\/\/iada.ubd.edu.bn\/index.php?rest_route=\/wp\/v2\/pages\/11061\/revisions\/11100"}],"wp:attachment":[{"href":"https:\/\/iada.ubd.edu.bn\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=11061"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}