This page contains information about the third party softwares which are included in the OSDDlinux. Debian files of the softwares are collected and a downloadable link is available from OSDDlinux repository. A user can download deb files from OSDDlinux repository and install to their local machine.
| Program | Purpose |
| AutodockTools | Graphical front-end for setting up and running AutoDock |
| Avogadro | Free cross platform molecule editor |
| Bowtie | Ultrafast memory-efficient short read aligner |
| BWA | Burrows Wheeler Aligner for mapping low divergent sequences against a large reference genome |
| Cain | Cain performs stochastic and deterministic simulations of chemical reactions |
| CD-HIT | Suite of programs designed to quickly group sequences |
| CHEMTOOL | A free software program for drawing chemical structural formulas |
| CIRCOS | # |
| CLUSTALX | Global multiple alignment program with graphical user interface |
| CONCAVITY | Ligand binding site prediction from protein sequence and structure |
| CUFFLINKS | # |
| EMBASSY | # |
| EMBOSS | Sequence analysis software package |
| FREEDIAMS | It can be used alone to prescribe and / or test drug interactions within a prescription |
| GABEDIT | A graphical user interface to computational chemistry packages like Gamess-US, Gaussian, Molcas, Molpro, MPQC, OpenMopac, Orca, PCGamess and Q-Chem |
| GARLIC | A free open source molecular viewer and editor |
| GCHEMPAINT | A 2D chemical structures editor for Gnome-2 Desktop |
| GROMACS | Molecular Dynamics Package |
| HMMER | A Software Package for biosequence analysis using profile HMMs |
| IGV | High-performance genomics data visualization and exploration |
| JALVIEW | Multiple sequence alignment editing and visualization |
| JMOL | An open source java viewer for chemical structures in 3D |
| KALZIUM | A program that visualizes the Periodic Table of Elements (PSE) and includes basic information about all common elements in the PSE. |
| LIBCDK-JAVA | CDK library with JAVA |
| LIBCDK-PERL | CDK library with perl |
| MOPAC7 | A general-purpose semiempirical molecular orbital package for the study of solid state and molecular structures and reactions |
| MPQC | Massively Parallel Quantum Chemistry Program |
| MUMMER | A system for rapidly aligning entire genomes, whether in complete or draft form |
| NCBI-TOOLS-X11 | Set of tools provided by NCBI |
| NJPLOT | A tree drawing program able to draw any binary tree expressed in the standard phylogenetic tree format |
| OPENBABEL | A chemical toolbox designed to speak the many languages of chemical data |
| PHYLIP | Phylogeny Inference Package computer programs for inferring phylogenies |
| PRIMER | Software for PCR PRIMER design |
| PYMOL | Molecular Visualization Software |
| PYTHON-BALLVIEW | Molecular Dynamics visualization program |
| RASMOL | Molecular Visualization Software |
| READSEQ | Reads and converts biosequences between a selection of common biological sequence formats |
| REVOLUTION-R | A software package with big data statistics, predictive modeling and machine learning capabilities |
| SAMTOOLS | A set of utilities for interacting with and post-processing short DNA sequence read alignments |
| GLIMMER | A system for finding genes in microbial DNA, especially the genomes of bacteria and archaea |
| UGENE | Free cross-platform bioinformatics software package for DNA and protein sequence analysis |
| VELVET | An algorithm package that has been designed to deal with de novo genome assembly and short read sequencing alignments |
| WEKA | A collection of machine learning algorithms for solving data mining problems |