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The aim of this page is to become a useful resource for biologists and students using Ubuntu (or any other) Linux. Please add information or comments.
目录
Ubuntu Biology Packages
Ubuntu Linux includes many packages useful for biologists.
- BioPerl 模板:Https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - a collection of Perl modules that are useful for programmers in bioinformatics/biology
- also see BioJava and BioPython
- Clustalw模板:Https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleM2.png - This program performs an alignment of multiple nucleotide or amino acid sequences. ClustalX 模板:Https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleM2.png is a GUI front end for ClustalW.
- Emboss 模板:Https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png- a suite of bioinformatics tools.
- Muscle模板:Https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - 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 模板:Https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleM2.png - A sequence editor with multiple alignment (via ClustalW) and other capabilities
- Phylip 模板:Https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleM2.png - A Package of programs for inferring phylogenies.
- Tree View X 模板:Https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - 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 模板:Https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - TREE-PUZZLE is a computer program to reconstruct phylogenetic trees from molecular sequence data by maximum likelihood.
- DIALIGN2 模板:Https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png- a command line tool to perform multiple alignment of protein or DNA sequences.
- UGENE 模板:Https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - an integrated bioinformatics 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 bioinformatics workstation. Bio-Linux provides more than 500 bioinformatics programs on an Ubuntu Linux base. There is a graphical menu for bioinformatics programs, as well as easy access to the Bio-Linux bioinformatics documentation system and sample data useful for testing programs.
Other Biology software not in Ubuntu
- Bioconductor - bioinformatics 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 bioinformatics 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.
- Visualization Toolkit (VTK) - an open-source software toolkit for image processing and data visualization.
- Code biofox - Code biofox aims at implementing various bioinformatics tools as an extension on the Firefox browser.
- FaMoZ - Software written in C and Tcl/Tk which uses likelihood calculations and simulations to perform parentage studies with dominant, codominant and cytoplasmic markers.
- <<Anchor(ITK)>>Insight Toolkit (ITK) 模板:Https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - 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.
