Ubuntu Biology Packages
Ubuntu Linux includes many packages useful for biologists.
- BioPerl:
http://packages.ubuntu.com/bioperl - a collection of Perl modules that are useful for programmers in bioinformatics/biology
also see BioJava and BioPython
- Clustalw:
http://packages.ubuntu.com/clustalw - This program performs an alignment of multiple nucleotide or amino acid sequences.
- ClustalX:
http://packages.ubuntu.com/clustalx is a GUI front end for ClustalW.
- Emboss:
http://packages.ubuntu.com/emboss- a suite of bioinformatic tools.
- Muscle
http://packages.ubuntu.com/muscle - A program for multiple alignment of protein sequences. MUSCLE stands for multiple sequence comparison by log-expectation. In the authors tests, MUSCLE achieved the highest scores of all tested programs on several alignment accuracy benchmarks, and is also one of the fastest programs out there
- Seaview
http://packages.ubuntu.com/seaview - A sequence editor with multiple alignment (via ClustalW) and other capabilities
- Phylip:
http://packages.ubuntu.com/phylip - A Package of programs for inferring phylogenies.
- Tree View X:
http://packages.ubuntu.com/treeviewx - Tree View X is an open source program to display phylogenetic trees on Linux, Unix, Mac OS X, and Windows platforms. It can read and display NEXUS and Newick format tree files (such as those output by PAUP*, ClustalX, TREE-PUZZLE, and other programs).
- Tree-puzzle:
http://packages.ubuntu.com/tree-puzzle - TREE-PUZZLE is a computer program to reconstruct phylogenetic trees from molecular sequence data by maximum likelihood.
- DIALIGN2:
http://packages.ubuntu.com/dialign- a command line tool to perform multiple alignment of protein or DNA sequences.
- UGENE:
http://packages.ubuntu.com/ugene - an integrated bioinformatic suite with handy visual interface. Integrates tool for HMM profile search, multiple sequence alignment, PCR primers design, protein secondary structure prediction and others.
Ubuntu Linux includes many packages useful for biologists.
http://packages.ubuntu.com/bioperl - a collection of Perl modules that are useful for programmers in bioinformatics/biology
also see BioJava and BioPython
http://packages.ubuntu.com/clustalw - This program performs an alignment of multiple nucleotide or amino acid sequences.
http://packages.ubuntu.com/clustalx is a GUI front end for ClustalW.
http://packages.ubuntu.com/emboss- a suite of bioinformatic tools.
http://packages.ubuntu.com/muscle - A program for multiple alignment of protein sequences. MUSCLE stands for multiple sequence comparison by log-expectation. In the authors tests, MUSCLE achieved the highest scores of all tested programs on several alignment accuracy benchmarks, and is also one of the fastest programs out there
http://packages.ubuntu.com/seaview - A sequence editor with multiple alignment (via ClustalW) and other capabilities
http://packages.ubuntu.com/phylip - A Package of programs for inferring phylogenies.
http://packages.ubuntu.com/treeviewx - Tree View X is an open source program to display phylogenetic trees on Linux, Unix, Mac OS X, and Windows platforms. It can read and display NEXUS and Newick format tree files (such as those output by PAUP*, ClustalX, TREE-PUZZLE, and other programs).
http://packages.ubuntu.com/tree-puzzle - TREE-PUZZLE is a computer program to reconstruct phylogenetic trees from molecular sequence data by maximum likelihood.
http://packages.ubuntu.com/dialign- a command line tool to perform multiple alignment of protein or DNA sequences.
http://packages.ubuntu.com/ugene - an integrated bioinformatic suite with handy visual interface. Integrates tool for HMM profile search, multiple sequence alignment, PCR primers design, protein secondary structure prediction and others.
Bio-Linux
Bio-Linux 5.0 - a fully featured, powerful, configurable and easy to maintain bioinformatic workstation. Bio-Linux provides more than 500 bioinformatic programs on an Ubuntu Linux base. There is a graphical menu for bioinformatic programs, as well as easy access to the Bio-Linux bioinformatic documentation system and sample data useful for testing programs.
Other Biology software not in Ubuntu
- Bioconductor -
bioinformatic tools.
- SciCraft -
Add-on to Octave, clones Simulink. Still in development, blocks have to be written by the user. It is supposed to specialize in bioinformatic functions
- LDhat -
LDhat is a package written in the C language for the analysis of recombination rates from population genetic data.
Structure Population genetic analysis of admixture. Uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed.
- Squint-
A sequence editor with automated alignment, translation, etc.
- simuPOP:
Highly modular and customizeable forward population genetic simulation software.
- ms:
The gold standard in coalescent simulations for population genetics.
- libsequence:
A C++ library designed to aid writing applications for genomics and evolutionary genetics. The library is intended to be viewed as a "BioC++" akin to the bioperl project, although the focus is on biological computation, such as the analysis of SNP data and data generated from coalescent simulation.
- Geneious-
NCBI-search, BLAST, sequence alignment, tree-building and publications all in a single intuitive application that updates your data.
- DAWG -
DNA Alignment With Gaps - A sequence simulation program similar to Seq-Gen, that allows the user to simulate the evolution of DNA sequences along a phylogeny. Includes all common models of sequence evolution as well as a model of indel formation.
- Mesquite -
Mesquite is a java based software for evolutionary biology, designed to help biologists analyze comparative data about organisms.
- Code biofox -
Code biofox aims at implementing various bioinformatic tools as an extension on the Firefox browser.
an open-source software toolkit for image processing and data visualization.
- FaMoZ -
Software written in C and Tcl/Tk which uses likelihood calculations and simulations to perform parentage studies with dominant, codominant and cytoplasmic markers.
- Insight Toolkit (ITK):
http://packages.ubuntu.com/insighttoolkit - an open-source software toolkit for performing registration and segmentation. Created to support the Visible Human Project.
unofficial Debian packages
- ApE -
A Plasmid Editor. ApE is an easy to use DNA sequence editor with many nice features. ApE is written in Tcl/Tk script. You will need to download the appropriate Tclkit version for your Linux distribution.
Unofficial Biology packages
Web Based Biology tools
Click here to Download Bioinformatic BOOKS
Other Biology software not in Ubuntu
bioinformatic tools.
Add-on to Octave, clones Simulink. Still in development, blocks have to be written by the user. It is supposed to specialize in bioinformatic functions
LDhat is a package written in the C language for the analysis of recombination rates from population genetic data.
A sequence editor with automated alignment, translation, etc.
Highly modular and customizeable forward population genetic simulation software.
The gold standard in coalescent simulations for population genetics.
A C++ library designed to aid writing applications for genomics and evolutionary genetics. The library is intended to be viewed as a "BioC++" akin to the bioperl project, although the focus is on biological computation, such as the analysis of SNP data and data generated from coalescent simulation.
NCBI-search, BLAST, sequence alignment, tree-building and publications all in a single intuitive application that updates your data.
DNA Alignment With Gaps - A sequence simulation program similar to Seq-Gen, that allows the user to simulate the evolution of DNA sequences along a phylogeny. Includes all common models of sequence evolution as well as a model of indel formation.
Mesquite is a java based software for evolutionary biology, designed to help biologists analyze comparative data about organisms.
Code biofox aims at implementing various bioinformatic tools as an extension on the Firefox browser.
an open-source software toolkit for image processing and data visualization.
Software written in C and Tcl/Tk which uses likelihood calculations and simulations to perform parentage studies with dominant, codominant and cytoplasmic markers.
http://packages.ubuntu.com/insighttoolkit - an open-source software toolkit for performing registration and segmentation. Created to support the Visible Human Project.
A Plasmid Editor. ApE is an easy to use DNA sequence editor with many nice features. ApE is written in Tcl/Tk script. You will need to download the appropriate Tclkit version for your Linux distribution.
Web Based Biology tools
