| Softwares | Description |
|---|
| Biopython 1.50 | Biopython is a set of freely available tools for biological computation written in Python by an international team of developers. |
| MIRA-2.8.2 | MIRA fragment assembly program |
| Vienna RNA 1.8.25 | The Vienna RNA Package consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures |
| Boxshade | This is a new release of the PASCAL program BOXSHADE , intended for shading multiple aligned sequence files. This is not a completely 'official' release, but makes the new facilities in v3.0 available until Kay can make time to tie up a full releas |
| concavity | Ligand binding site prediction from protein sequence and structure |
| Hhsuite | A set of programs for protein sequence homology detection by iterative HMM-HMM comparison for computational biology like PSI-BLAST |
| Cain | Cain performs stochastic and deterministic simulations of chemical reactions. It can spawn multiple simulation processes to utilize multi-core computers. It stores models, simulation parameters, and simulation results in an XML format. In addition, SBML models can be imported and exported. The models and simulation parameters can be read from input files or edited within the program. |
| Python-rdkit | This document is intended to provide an overview of how one can use the RDKit functionality from Python. It’s not comprehensive and it’s not a manual. |
| Raccoon | Raccoon is a graphical interface for preparing AutoDock virtual screenings. |
| Freediams | It is mainly developed by medical doctors and is intended for use by these same professionals. It can be used alone to prescribe and / or test drug interactions within a prescription. It can be linked to any application thanks to its command line parameters. |
| FreemedForms-Freedata | pharmaceutical drug prescription and interaction manager |
| OpenClinica | OpenClinica is the world's leading open source clinical trials software for electronic data capture (EDC) and clinical data management (CDM) |
| Abinit | ABINIT is a package whose main program allows one to find the total energy, charge density and electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a planewave or wavelet basis |
| Openmax | OpenMAX™ is a royalty-free, cross-platform API that provides comprehensive streaming media codec and application portability by enabling accelerated multimedia components to be developed, integrated and programmed across multiple operating systems and silicon platforms. |
| Ccwatcher | ccwatcher monitors the progress of computational chemistry calculations during their runtime. It parses important output and plots SCF energies. ccwatcher is platform-independent thanks to Python and the Qt Toolkit. |
| Kalzium | Kalzium is your digital replacement for the periodic table on paper. It ss a program that visualizes the Periodic Table of Elements (PSE) and includes basic information about all common elements in the PSE. It has a gained much more functions over time. |
| Gabedit | abedit is a graphical user interface to computational chemistry packages like Gamess-US, Gaussian, Molcas, Molpro, MPQC, OpenMopac, Orca, PCGamess and Q-Chem |
| Gchem3d | The Gnome Chemistry Utils provide some programs and library containing GTK widgets and some C++ classes related to chemistry. |
| Gchemcalc | The Gnome Chemistry Utils provide some programs and library containing GTK widgets and some C++ classes related to chemistry. |
| GChemPaint | GChemPaint allows you to draw and display 2D chemical structures |
| Gnome Chemistry Utils | The Gnome Chemistry Utils provide some programs and library containing GTK widgets and some C++ classes related to chemistry |
| Mopac7r | MOPAC 7 is public domain and the source code mopac7.tar.gz can be obtained from the WebMO website. |
| Mpqc | MPQC is the Massively Parallel Quantum Chemistry Program. It computes properties of atoms and molecules from first principles using the time independent Schrödinger equation. |
| Viewmol | Viewmol is an open source graphical front end for computational chemistry programs. |
| XDrawChem | XDrawChem is a two-dimensional molecule drawing program for Unix operating systems. It is similar in functionality to other molecule drawing programs such as ChemDraw (TM, CambridgeSoft). |
| PSI4 | PSI4 is an electronic structure package which emphasizes highly accurate wave function methods, such as coupled cluster and configuration interaction. |
| ABySS 1.3.5 | de novo, parallel, sequence assembler for short reads |
| ampliconnoise 1.28 | Programs for the removal of noise from 454 sequenced PCR amplicons |
| arb 5.5 | Integrated package for sequence database handling and analysis |
| artemis 13.2 | Free genome viewer and annotation tool |
| assembly-conversion-tools 0.01 | Conversion tools for handling 454 assemblies. |
| beam2 0.1+20101008 | SNP-SNP interaction association mapping based on SNP-block models |
| bedtools 2.17.0 | suite of utilities for comparing genomic features |
| bioperl 1.6.901 | Perl tools for computational molecular biology |
| bioperl-run 1.6.9 | BioPerl wrappers: scripts |
| biosquid 1.9g+cvs20050121 | utilities for biological sequence analysis |
| bitseq 0.4.3 | Bayesian Inference of Transcripts from Sequencing Data |
| blimps-utils 3.9 | blocks database improved searcher |
| blixem 3.1.1 | Interactive browser for viewing pairwise Blast results. |
| bowtie 1.0.0-1 | ultrafast memory-efficient short read aligner |
| bowtie2 2.1.0-1 | ultrafast memory-efficient short read aligner |
| bwa 0.6.1 | Burrows-Wheeler Aligner |
| cap3 20080520 | This software allows you to assemble a set of contiguous sequences (contigs) with the CAP3 program. |
| catchall 3.0.1 | Analyze data about microbial species abundance |
| cd-hit 4.6.1-2012-08-27 | suite of programs designed to quickly group sequences |
| cdbfasta 20100722 | Constant DataBase indexing and retrieval tools for multi-FASTA files |
| chimeraslayer 20101212 | detects likely chimeras in PCR amplified DNA |
| clc sequence viewer 6.4 | CLC Free Sequence Viewer |
| clustalw 2.1+lgpl | global multiple nucleotide or peptide sequence alignment |
| clustalx 2.1+lgpl | CLUSTAL X is a new windows interface for the widely-used progressive multiple sequence alignment program CLUSTAL W |
| cortex-con 0.05 | efficient and low-memory software for consensus genome assembly |
| cufflinks 2.1.1 | Transcript assembly, differential expression and regulation for RNA-Seq |
| cytoscape 1.2.7.0 | Platform for visualizing complex-networks and integrating these with attribute data |
| Dendroscope 3 | Software for visualizing phylogenetic trees and rooted networks. |
| dialign 2.2.1 | Segment-based multiple sequence alignment |
| dotter 3.1 | Graphical dotplot program for detailed comparison of two sequences |
| embassy-domalign 0.1.650 | Extra EMBOSS commands for protein domain alignment |
| embassy-domsearch 1:0.1.650 | Extra EMBOSS commands to search for protein domains |
| emboss 6.5.7 | european molecular biology open software suite |
| estscan2 2.1 | detects coding regions of DNA sequences |
| fastdnaml 1.2.2 | Tool for construction of phylogenetic trees of DNA sequences |
| fastqc 0.10.1 | A quality control application for high throughput sequence data |
| fasttree 2.1.3 | Infers approximately-maximum-likelihood phylogenetic trees |
| fastx-toolkit 0.0.13.1 | FASTQ/A short nucleotide reads pre-processing tools |
| galaxy-server 1.bl.py27.20120718 | A web-based analysis environment |
| geneious 5.5.7 | Geneious Basic workbench from Biomatters |
| glam2 4.8.1 | gapped protein motifs from unaligned sequences |
| glimmer3 3.02 | System for finding genes in microbial DNA. |
| gnx-tools 0.1+20120305 | Basic genome assembly statistic tool to calculate Nx values e.g. N50,N10,NG50 |
| handlebar 2.2.2 | Handlebar is a database for storing data about barcodes and acessing the data via a web front-end. |
| happy 1.2 | Multipoint QTL Mapping in Genetically Heterogeneous Animals |
| hmmer 3.1b1 | profile hidden Markov models for protein sequence analysis |
| hmmer2 2.3.2 | profile hidden Markov models for protein sequence analysis |
| hmmer2-pvm 2.3.2 | HMMER programs with PVM (Parallel Virtual Machine) support |
| hyphy 2.1+20111219 | analysis of genetic sequences using multiple techniques |
| infernal 1.0.2 | inference of RNA secondary structural alignments |
| io-lib-tools 1.13.1 | command line tools provided with Staden io-lib |
| jalview 1:2.7.0 | a Java multiple alignment editor |
| JELLYFISH | ELLYFISH is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence |
| jemboss 6.5.7 | graphical user interface to EMBOSS |
| jmotu 1.0.6 | Clusters barcode DNA sequence data into molecular operational taxonomic units |
| jprofilegrid 2.0.5 | Multiple sequence alignment tool that generates ProfileGrids |
| lastz 1.02.00 | Aligns two DNA sequences, inferring appropriate parameters automatically |
| libbiojava-java 1:1.7.1 | Java API to biological data and applications |
| libbiojava-java-demos 1:1.7.1 | Example programs for BioJava |
| lucy 1.19p | Preparation of raw DNA sequence fragments for sequence assembly |
| macs 2.0.9.1 | Model-based Analysis of ChIP-Seq on short reads sequencers |
| mafft 7.037 | Multiple alignment program for amino acid or nucleotide sequences |
| maq 0.7.1 | maps short fixed-length polymorphic DNA sequence reads to reference sequences |
| maxd 2.3.0 | maxd is a data warehouse and visualisation environment for genomic expression data. |
| meme 4.8.1 | search for common motifs in DNA or protein sequences |
| mesquite 2.74 | Software for evolutionary biology. |
| microbiomeutil 20101212 | Microbiome Analysis Utilities |
| mira-3rdparty 20120706 | Additional useful tools to accomapany the MIRA assembler |
| mira-assembler 3.4.1.1 | Whole Genome Shotgun and EST Sequence Assembler |
| mothur 1.30.2+repack | sequence analysis suite for research on microbiota |
| mrbayes 3.2.1+dfsg+repack | Bayesian Inference of Phylogeny |
| mrbayes-mpi 3.2.1+dfsg+repack | Bayesian Inference of Phylogeny - mpi version |
| mspcrunch 2.5 | a BLAST post-processing filter. |
| mummer 3.23~dfsg | Efficient sequence alignment of full genomes |
| muscle 1:3.8.31 | Multiple alignment program of protein sequences |
| mview 1.51 | Multiple alignment viewer for sequence database search results. |
| nast-ier 20101212 | NAST-based DNA alignment tool |
| natefoo-add-scores 0.1+20101006 | small helper application used by Galaxy server |
| natefoo-taxonomy 0.1+20101102 | small taxonomy applications used by Galaxy server |
| ncbi-blast+-static 2.2.26 | next generation suite of BLAST sequence search tools |
| ncbi-seg 0.0.20000620 | tool to mask segments of low compositional complexity in amino acid sequences |
| ncbi-tools-x11 6.1.20110713 | NCBI libraries for biology applications (X-based utilities) |
| njplot 2.3 | phylogenetic tree drawing program |
| norsnet 1.0.16 | tool to identify unstructured loops in proteins |
| oligoarray 2.1 | Computes oligonucleotides for microarray construction |
| oligoarrayaux 3.7 | Free software that is required for the OligoArray2.1 software. |
| omegamap 0.5 | Detects natural selection and recombination in DNA or RNA sequences. |
| paml 4.5 | Phylogenetic Analysis by Maximum Likelihood (PAML) |
| pass2 0.1+20101008 | Peak calling in ChIP data based on Poisson de-clumping |
| perm 0.3.9 | Efficient mapping of short reads with periodic spaced seeds |
| pfaat 1.0.034 | Sequence alignment editor designed for protein family analysis. |
| PHYLIP NEW-3.67 | package of programs for inferring phylogenies |
| picard-tools 1.91 | Command line tools to manipulate SAM and BAM files |
| plymouth-theme 7 | Boot splash for Ubuntu |
| prank 0.0.120716 | Probabilistic Alignment Kit for DNA, codon and amino-acid sequences |
| predictnls 1.0.20 | prediction and analysis of protein nuclear localization signals |
| predictprotein 1.0.86 | suite of protein sequence analysis tools |
| primer3 2.2.3 | Tool to design flanking oligo nucleotides for DNA amplification |
| probcons 1.12 | PROBabilistic CONSistency-based multiple sequence alignment |
| profbval 1.0.22 | predictor of flexible/rigid protein residues from sequence |
| profisis 1.0.11 | prediction of protein-protein interaction sites from sequence |
| profphd 1.0.39 | secondary structure and solvent accessibility predictor |
| proftmb 1.1.10 | per-residue prediction of bacterial transmembrane beta barrels |
| qiime 1.7.0 | Quantitative Insights Into Microbial Ecology |
| r-base 3.0.1 | GNU R statistical computation and graphics system |
| r-base-core 3.0.1 | GNU R core of statistical computation and graphics system |
| r-base-dev 3.0.1 | GNU R installation of auxiliary GNU R packages |
| r-bioc-biobase 2.20.0 | GNU R package "Biobase: Base functions for Bioconductor" |
| r-bioc-biocgenerics 0.6.0 | GNU R package "Generic functions for Bioconductor" |
| r-bioc-bitseq 1.4.2 | Bioconductor package "Transcript expression inference and differential |
| r-bioc-edger 3.2.3 | GNU R package "Empirical analysis of digital gene |
| r-bioc-genomicranges 1.12.2 | GNU R package "Representation and manipulation of genomic |
| r-bioc-limma 3.16.1 | GNU R package "Linear Models for Microarray Data" |
| r-bioc-qvalue 1:1.34.0 | Bioconductor package "Q-value estimation for false discovery rate control" |
| r-bioc-rsamtools 1.12.2 | GNU R package "Binary alignment (BAM), variant call (BCF), |
| r-bioc-zlibbioc 1.6.0 | GNU R package "An R packaged zlib-1.2.5" |
| r-cran-bitops 1.0-5 | GNU R package "Bitwise Operations" |
| r-cran-catools 1.14 | GNU R package "Tools: moving window statistics, GIF, |
| r-cran-cluster 1.14.4 | GNU R package for cluster analysis by Rousseeuw et al |
| r-cran-dbi 0.2-6 | GNU R package providing a generic database interface |
| r-cran-digest 0.6.3 | GNU R package "Create cryptographic hash digests of R objects" |
| r-cran-evaluate 0.4.3 | GNU R package "Parsing and evaluation tools that provide |
| r-cran-gdata 2.12.0.2 | GNU R package with data manipulation tools by Greg Warnes et al |
| r-cran-gee 4.13r18 | GNU R package "Generalized Estimation Equation solver" |
| r-cran-gplots 2.11.0.1 | GNU R package with tools for plotting data by Greg Warnes et al |
| r-cran-gtools 2.7.1 | GNU R package with R programming tools by Greg Warnes et al |
| r-cran-lattice 0.20-15 | GNU R package "Lattice Graphics" |
| r-cran-samr 2 | GNU R package "SAM: Significance Analysis of Microarrays" |
| r-cran-sp 1:1.0-9 | GNU R classes and methods for spatial data |
| r-cran-stringr 0.6.2 | GNU R package "Make it easier to work with strings." |
| r-cran-tcltk2 1.2.5 | GNU R package "Tcl/Tk Additions" |
| r-cran-testthat 0.7.1 | GNU R package "Testthat code. Tools to make testing fun :)" |
| r-cran-vegan 2.0-7 | Community Ecology Package for R |
| r-cran-wavethresh 4.6.2 | GNU R package "Wavelets statistics and transforms." |
| r-cran-xml | GNU R package "Tools for parsing and generating XML within |
| r-cran-xtable 1:1.7-1 | GNU R coerce data to LaTeX and HTML tables |
| rasmol 2.7.5 | Randomized Axelerated Maximum Likelihood of phylogenetic trees |
| ray 2.2.0 | parallel genome assemblies for parallel DNA sequencing |
| rbs-finder 1 | A program to find Ribosomal binding sites. |
| rdp-classifier 2.5+repack | taxonomic assignment from next generation sequencing |
| readseq 1 | Conversion between sequence formats |
| samtools 0.1.18 | processing sequence alignments in SAM and BAM formats |
| scythe 0.991 | Bayesian adapter trimmer for nextgen sequence reads |
| seqan-apps 1.3.1 | C++ library for the analysis of biological sequences |
| sickle 0.94 | windowed adaptive trimming tool for FASTQ files using quality |
| sift 4.0.3b | predicts if a substitution in a protein has a phenotypic effect |
| splitstree 4.13.1 | Analysis and visualisation tool for distance data from biological sequences |
| sputnik-mononucleotide 0.1+20101005 | Searches dna sequence files in Fasta format for microsatellite repeat. |
| squint 1.02 | Java-based multiple alignment program and editor |
| ssake 3.8 | genomics application for assembling millions of very short DNA sequences |
| staden 2006.1.7.0+1.11.6 | A suite of tools for sequence analysis. |
| stars 1.2a | STARS is an alternative interface to Staden. |
| t-coffee 9.03.r1318 | Multiple Sequence Alignment |
| tablet 1.12.03.26 | Graphical viewer for next gen sequence assemblies and alignments |
| taverna 1.7 | Workflow tool that make use of web services. |
| tetra 1.0b3 | tetranucleotide frequency calculator with GUI |
| tigr-glimmer 3.02 | Gene detection in archea and bacteria |
| tophat 2.0.8 | fast splice junction mapper for RNA-Seq reads |
| transterm-hp 2.07 | Transterm finds rho-independent transcription terminators in bacterial genomes. |
| transtermhp 2.09 | find rho-independent transcription terminators in bacterial genomes |
| tree-puzzle 5.2 | Reconstruction of phylogenetic trees by maximum likelihood |
| tree-puzzle-doc 5.2 | Reconstruction of phylogenetic trees by maximum likelihood |
| treeviewx 0.5.1+20100823 | Displays and prints phylogenetic trees |
| trnascan 1.21 | tRNAscan-SE searches for tRNA genes in genomic sequences. |
| trnascan-se 1.3.1 | search for tRNA genes in genomic sequences |
| ugene 1.9.8+repack | integrated bioinformatics toolkit |
| velvet 1.2.08 | Example data for the Velvet sequence assembler |
| velvet-long 1.2.08 | Nucleic acid sequence assembler for very short reads, long version |
| WebLogo 3.1 | A tool for creating sequence logos from biological sequence alignments |
| zsh 1 | Z-Shell |
| ClustalX 2.0, | Interactive program for multiple sequence alignment. Friendly GUI. |
| Cn3D | Structure visualizer for NCBI's Entrez retrieval service. |
| EMBOSS tools | A suite of program for sequence and pattern alignment, protein motif identification and more. |
| Genome softwares | Genome related softwares. |
| GP/Arka | Programs for manipulation of DNA/RNA/protein sequences. |
| NJPlot | A binary tree drawing program for phylogenetic trees. |
| Ramachandran Plot Explorer | Protein visualizer |
| Raster3D | Program for high quality image output for biomolecules. |
| SeaView | SeaView is a graphical multiple sequence alignment. |
| TINKER | Software tools for molecular modeling (MD). |
