Welcome to Bioinformatics resources

The main goal of the OSDDlinux is to provides a platform for Bioinformatician, Biologists and students to provides basic infrastructure and tools related to bioinformatics resources. Here we provided some commonly used tools and techniques used in bioinformatics field.

On this portal user find different resources related to bioinformatics field from different group:

Web services in bioinformatics
PDB GeneBank
ExPASy UniProt

Sequence analysis tools and techniques
BLAST Psi-Blast
BlastClust HMMER
CD-HIT ClustalW

Genome annotation
MEGA Prokka
David FTG

Other packages
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 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 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 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 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 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 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 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).