Newbies What Next ? News Forums Calendar
Home | Register | News | Forums | Portal Pages | MyLinks | New | Hot | Link Us


 Category Gateway
More Options

LinuxLinks News
 · Fun to Play Open Source Real-Time Strategy Games Fight for Glory
 · Grasp PL/SQL/pgSQL Programming with Free Books
 · Fun to Play Open Source First-Person Shooter Games
 · Grasp Prolog Programming with Free Books
 · Le Grand Fromage of Open Source
 · 8 Insanely Addictive Multi-Platform Open Source Simulation Games
 · 5 Best Open Source Multi-Platform Data Science Notebook Software
 · Learn Logo Programming with No Charge Books
 · Learn TeX Programming with Free Books
 · Grasp LaTeX Programming with Free Books


Latest Links

Top : Software : Scientific : Biology : Genetics

Fun to Play Open Source Real-Time Strategy Games Fight for Glory
RTS games have a large fan base since their inception. This game genre requires cunning, creativity, and the ability to devise innovative strategies to usurp your opponents. Some of the best known proprietary RTS series are Warcraft, Starcraft, Command & Conquer, and Age of Empires.

(Read more)
WeeChat is a fast and light IRC client for many operating systems. Everything can be done with a keyboard, and it is customizable and extensible with scripts. Read more


  • AceDB
    AceDB is a genome database designed specifically for handling bioinformatic data flexibly. It includes tools designed to manipulate genomic data, but is increasingly also used for non-biological data.
  • autoseq
    autoseq is a small package of base calling software for ABI automated DNA sequencers. It is intended as a starting point for researchers interested in new base calling algorithms. It implements a simple Bayesian peak identification algorithm which is experimental and does not generally perform better than software provided by ABI.
  • Blossoc
    Blossoc is a linkage disequilibrium association mapping tool that attempts to build (perfect) genealogies for each site in the input and score these according to non-random clustering of affected individuals, and judge high-scoring areas as likely candidates for containing disease affecting variation.
  • COVE
    COVE is an implementation of stochastic context free grammar methods for RNA sequence/structure analysis.
    DNA-GUI reads image files holding pictures of DNA gel electrophoreses, assigns lanes, finds bands, and, given the proper standards, processes the pictures and computes sizes for each band identified (by the program or manually).
  • DNPTrapper
    DNPTrapper is an assembly editing and visualization tool specifically designed for manual analysis and finishing of repeated regions. The program allows the user to view whole repeat regions at once and to edit assembly errors manually by drag and drop. It implements and visualizes the results of a statistical method that detects defined nucleotide positions (DNPs, representing single base differences between repeat units) in the presence of sequencing errors.
  • Dotter
    Dotter draws a dotplot of two sequences (DNA or Protein) on the screen. It has a 'Greyramp Tool' to interactively adjust the score cutoffs for displaying dots, so the separation between noise and signal can be fine-tuned interactively. It also features a crosshair, at which the residue-alignment of the two sequences will be displayed in the 'Alignment tool'.
  • ESTScan
    ESTScan is a program that can detect coding regions in DNA sequences, even if they are of low quality. ESTScan will also detect and correct sequencing errors that lead to frameshifts.
  • Fast Genetic Algorithm
    FGA is a simple yet powerful implementation of a general genetic algorithm, and provides many types of crossover and selection procedures. It is suitable to solve mathematical problems such as combinatorical optimization ones, as well as to build artificial life simulations.
  • fastDNAml
    fastDNAml is for estimating maximum likelihood phylogenetic trees from nucleotide sequences.
    FASTLINK is a significantly modified and improved version of the main programs of LINKAGE that runs much faster sequentially, can run in parallel, allows the user to recover gracefully from a computer crash, and provides abundant new documentation.
  • FinchTV
    Geospiza's FinchTV is the popular way to view DNA sequence traces on Linux, Mac OSX, Windows, and Solaris. FinchTV started as the only chromatogram viewer that can display an entire trace in a scalable multipane view. Now it leads again with raw data views, BLAST searching and the ability to reverse complement sequences and traces.
  • GeneRecon
    GeneRecon is a software package for linkage disequilibrium mapping using coalescent theory. It is based on a Bayesian Markov-chain Monte Carlo (MCMC) method for fine-scale linkage-disequilibrium gene mapping using high-density marker maps. GeneRecon explicitly models the genealogy of a sample of the case chromosomes in the vicinity of a disease locus. Given case and control data in the form of genotype or haplotype information, it estimates a number of parameters, most importantly, the disease position.
  • Genomorama
    Genomorama is a software program for interactively displaying multiple genomes. It provides a powerful yet easy to use interface that leverages the visualization power of modern computers (via OpenGL) and the substantial bioinformatic infrastructure provided by the NCBI (via the NCBI C toolkit). Genomorama is written in portable, highly optimized C++ and comes in three "flavors" that allow it to run natively on (most) modern operating systems: OS X (using Carbon), Microsoft Windows (using MFC), and Linux (using Motif). Executables and source code are freely provided for all flavors.
  • HapCluster++
    HapCluster++ is a software package for linkage disequilibrium mapping using coalescent theory. It is based on a Bayesian Markov-chain Monte Carlo (MCMC) method for fine-scale linkage-disequilibrium gene mapping using high-density marker maps. HapCluster++ is a C++ implementation of the method described in the paper below (the original implementation was in R).
  • Hidden Markov Model Toolkit
    The Hidden Markov Model Toolkit (HTK) is a portable toolkit for building and manipulating hidden Markov models. HTK is primarily used for speech recognition research, although it has been used for numerous other applications. HTK consists of a set of library modules and tools available in C source form. The tools provide sophisticated facilities for speech analysis, HMM training, testing, and results analysis. The software supports HMMs using both continuous density mixture Gaussians and discrete distributions, and can be used to build complex HMM systems.
    Profile hidden Markov models (profile HMMs) can be used to do sensitive database searching using statistical descriptions of a sequence family's consensus. HMMER is a freely distributable implementation of profile HMM software for protein sequence analysis.
  • Infernal
    Infernal is an implementation of "covariance models" (CMs), which are statistical models of RNA secondary structure and sequence consensus. You give Infernal a multiple sequence alignment of a conserved structural RNA family, annotated with the consensus secondary structure.
  • Mauve
    Mauve constructs global multiple alignments of rearranged genome sequences. It also provides an interactive display of multi-species sequence conservation and any annotated features in those genomes. It can be applied for sequence comparison of both finished or incomplete genomes in multiple contigs. The resulting display is useful for identifying functional chromosomal regions under selective pressure and for performing ortholog assignment based on conserved gene order. Mauve writes global alignments in eXtended Multi-FastA (XMFA) format, a phylogenetic guide tree in Newick format, and the location of genomic islands. It identifies the breakpoints of genomic rearrangement and can provide a reduction of the genomes to a signed permutation matrix suitable for inference of rearrangement history.
  • PhenoTips
    PhenoTips is a tool for collecting and analyzing phenotypic information for patients with genetic disorders.
    PKNOTS demonstrates a dynamic programming algorithm for globally optimal RNA pseudoknot prediction.
  • QRNA
    A prototype ncRNA genefinder. QRNA uses comparative genome sequence analysis to detect conserved RNA secondary structures, including both ncRNA genes and cis-regulatory RNA structures.
  • QualTrace
    (commercial) QualTrace offers a real time estimate of DNA sequence trace quality for the ABI 3730 sequencer. It can be used to identify production problems that affect read length and success rate.
    RECON is a package for automated de novo identification of repeat families from genomic sequences.
  • RepeatFinder
    RepeatFinder is a tool for finding repeating segments of DNA called motifs and then parsing them so that no repeating segments overlap - it is an exclusive matching algorithm where any part of the original DNA string is associated with one and only one match.
    RNABOB is an implementation of D. Gautheret's RNAMOT, but with a different underlying algorithm using a nondeterministic finite state machine with node rewriting rules.
  • tRNAscan-SE
    tRNAscan-SE detects ~99% of eukaryotic nuclear or prokaryotic tRNA genes, with a false positive rate of less than one per 15 gigabases, and with a search speed of about 30 kb/second. It was implemented for large-scale human genome sequence analysis, but is applicable to other DNAs as well.
  • Visomics
    Visomics is an open-source tool for the exploration of biological omics data with a focus on genomics, proteomics, transcriptomics, and metabolomics.

Matching Content

Share this Page
Bookmark and Share
Submit this page to popular social networks such as Digg, Twitter, StumbleUpon and more.

My LinuxLinks
  • Bookmarked links
  • Emailed Newsletter
  • Your own profile

  • Top Applications
    100 Essential Apps
    All Group Tests

    Top Free Software
    5 Office Suites
    3 Lean Desktops
    7 Document Processors
    4 Distraction Free Tools
    9 Project Management
    4 Business Solutions
    9 Groupware Apps
    14 File Managers
    10 Databases
    21 Backup Tools
    21 Productivity Tools
    5 Note Taking Apps
    9 Terminal Emulators
    21 Financial Tools
    5 Bitcoin Clients
    21 Text Editors
    21 Video Emulators
    21 Home Emulators
    42 Graphics Apps
    6 CAD Apps
    42 Scientific Apps
    10 Web Browsers
    42 Email Apps
    12 Instant Messaging
    10 IRC Clients
    7 Twitter Clients
    12 News Aggregators
    11 VoIP Apps
    42 Best Games
    9 Steam Games
    42 Audio Apps
    5 Music Streaming
    42 Video Apps
    5 YouTube Tools
    80 Security Apps
    9 System Monitoring
    8 Geometry Apps
    Free Console Apps
    14 Multimedia
    4 Audio Grabbers
    9 Internet Apps
    3 HTTP Clients
    5 File Managers
    8 Compilers
    9 IDEs
    9 Debuggers
    7 Revision Control Apps
    6 Doc Generators
    Free Web Software
    21 Web CMS
    14 Wiki Engines
    8 Blog Apps
    6 eCommerce Apps
    5 Human Resource Apps
    10 ERP
    10 CRM
    6 Data Warehouse Apps
    8 Business Intelligence
    6 Point-of-Sale

    Other Articles
    Migrating from Windows
    Back up your data
    20 Free Linux Books
    24 Beginner Books
    12 Shell Scripting Books

    Web Calendar
    Linux Licenses

    Advertise at


    Add Link | Modify Link | About | FAQ | Guide | Privacy | Awards | Contact |
    Portal Version 0.7. Intel Blade.
    Comments to the webmaster are welcome.
    Copyright 2009 All rights reserved.