“UbuntuHelp:UbuntuScience/Biology”的版本间的差异
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{{From|https://help.ubuntu.com/community/UbuntuScience/Biology}} | {{From|https://help.ubuntu.com/community/UbuntuScience/Biology}} | ||
{{Languages|UbuntuHelp:UbuntuScience/Biology}} | {{Languages|UbuntuHelp:UbuntuScience/Biology}} | ||
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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. | 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. | ||
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=== Ubuntu Biology Packages === | === Ubuntu Biology Packages === | ||
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Ubuntu Linux includes many packages useful for biologists. | Ubuntu Linux includes many packages useful for biologists. | ||
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* [http://www.bioperl.org BioPerl] [http://packages.ubuntu.com/bioperl 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 | * [http://www.bioperl.org BioPerl] [http://packages.ubuntu.com/bioperl 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 [http://www.biojava.org BioJava] and [http://www.biopython.org BioPython] | + | ** also see [http://www.biojava.org BioJava] and [http://www.biopython.org BioPython] |
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* [http://www.ebi.ac.uk/clustalw/ Clustalw][http://packages.ubuntu.com/clustalw 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 is a gui front end for clustalw. | * [http://www.ebi.ac.uk/clustalw/ Clustalw][http://packages.ubuntu.com/clustalw 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 is a gui front end for clustalw. | ||
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* [http://www.drive5.com/muscle/ Muscle][http://packages.ubuntu.com/muscle https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png] - A program for multiple alignment of protein sequences. MUSCLE | * [http://www.drive5.com/muscle/ Muscle][http://packages.ubuntu.com/muscle 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 | 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 | programs on several alignment accuracy benchmarks, and is also one of the fastest programs out there | ||
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* [http://pbil.univ-lyon1.fr/software/seaview.html Seaview] [http://packages.ubuntu.com/seaview https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleM2.png] - A sequence editor with multiple alignment (via CLustalW) and other capabilities | * [http://pbil.univ-lyon1.fr/software/seaview.html Seaview] [http://packages.ubuntu.com/seaview https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleM2.png] - A sequence editor with multiple alignment (via CLustalW) and other capabilities | ||
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* [http://evolution.genetics.washington.edu/phylip.html Phylip] [http://packages.ubuntu.com/phylip https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleM2.png] - A Package of programs for inferring phylogenies. | * [http://evolution.genetics.washington.edu/phylip.html Phylip] [http://packages.ubuntu.com/phylip https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleM2.png] - A Package of programs for inferring phylogenies. | ||
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* [http://darwin.zoology.gla.ac.uk/%7Erpage/treeviewx/index.html Tree View X] [http://packages.ubuntu.com/treeviewx 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). | * [http://darwin.zoology.gla.ac.uk/%7Erpage/treeviewx/index.html Tree View X] [http://packages.ubuntu.com/treeviewx 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). | ||
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* [http://www.tree-puzzle.de/ Tree-puzzle] [http://packages.ubuntu.com/tree-puzzle 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. | * [http://www.tree-puzzle.de/ Tree-puzzle] [http://packages.ubuntu.com/tree-puzzle 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. | ||
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* [http://dialign.gobics.de/ DIALIGN2] [http://packages.ubuntu.com/dialign 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. | * [http://dialign.gobics.de/ DIALIGN2] [http://packages.ubuntu.com/dialign 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. | ||
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=== Other Biology software not in Ubuntu === | === Other Biology software not in Ubuntu === | ||
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* [http://www.bioconductor.org/ Bioconductor] - bioinformatics tools. | * [http://www.bioconductor.org/ Bioconductor] - bioinformatics tools. | ||
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* [http://www.emboss.org Emboss] - a suite of bioinformatics tools. | * [http://www.emboss.org Emboss] - a suite of bioinformatics tools. | ||
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* [http://www.scicraft.org/ SciCraft] - Addon to Octave, clones Simulink. Still in developement, blocks have to be written by the user. It is supposed to specialize in bioinformatics functions | * [http://www.scicraft.org/ SciCraft] - Addon to Octave, clones Simulink. Still in developement, blocks have to be written by the user. It is supposed to specialize in bioinformatics functions | ||
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* [http://www.stats.ox.ac.uk/~mcvean/LDhat/ LDhat] LDhat is a package written in the C language for the analysis of recombination rates from population genetic data. | * [http://www.stats.ox.ac.uk/~mcvean/LDhat/ LDhat] LDhat is a package written in the C language for the analysis of recombination rates from population genetic data. | ||
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* [http://pritch.bsd.uchicago.edu/structure.html Structure] Populationg 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. | * [http://pritch.bsd.uchicago.edu/structure.html Structure] Populationg 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. | ||
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* [http://www.cebl.auckland.ac.nz/index.php?target=software&item=6 Squint]- A sequence editor with automated alignment, translation, etc. | * [http://www.cebl.auckland.ac.nz/index.php?target=software&item=6 Squint]- A sequence editor with automated alignment, translation, etc. | ||
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* [http://bp6.stat.rice.edu:8080/simuPOP/ simuPOP] Highly modular and customizeable forward population genetic simulation software. | * [http://bp6.stat.rice.edu:8080/simuPOP/ simuPOP] Highly modular and customizeable forward population genetic simulation software. | ||
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* [http://home.uchicago.edu/~rhudson1/source/mksamples.html ms] The gold standard in coalescent simulations for population genetics. | * [http://home.uchicago.edu/~rhudson1/source/mksamples.html ms] The gold standard in coalescent simulations for population genetics. | ||
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* [http://molpopgen.org/software/libsequence_html/libsequence.htm 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. | * [http://molpopgen.org/software/libsequence_html/libsequence.htm 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. | ||
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* [http://www.geneious.com/ Geneious]- NCBI-search, BLAST, sequence alignment, tree-building and publications all in a single intuitive application that updates your data. | * [http://www.geneious.com/ Geneious]- NCBI-search, BLAST, sequence alignment, tree-building and publications all in a single intuitive application that updates your data. | ||
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* [http://scit.us/projects/dawg/ 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. | * [http://scit.us/projects/dawg/ 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. | ||
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* [http://mesquiteproject.org/mesquite/mesquite.html Mesquite] - Mesquite is a java based software for evolutionary biology, designed to help biologists analyze comparative data about organisms. | * [http://mesquiteproject.org/mesquite/mesquite.html Mesquite] - Mesquite is a java based software for evolutionary biology, designed to help biologists analyze comparative data about organisms. | ||
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* [http://www.vtk.org/ Visualization Toolkit (VTK)] - an open-source software toolkit for image processing and data visualization. | * [http://www.vtk.org/ Visualization Toolkit (VTK)] - an open-source software toolkit for image processing and data visualization. | ||
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* [http://schematron.unl.edu/biofox/index.html Code biofox] - Code biofox aims at implementing various bioinformatics tools as an extension on the Firefox browser. | * [http://schematron.unl.edu/biofox/index.html Code biofox] - Code biofox aims at implementing various bioinformatics tools as an extension on the Firefox browser. | ||
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* [http://http://www.pierroton.inra.fr/genetics/labo/Software/Famoz/index.html FaMoZ] - Software written in C and Tcl/Tk which uses likelihood calculations and simulations to perform parentage studies with dominant, codominant and cytoplasmic markers. | * [http://http://www.pierroton.inra.fr/genetics/labo/Software/Famoz/index.html FaMoZ] - Software written in C and Tcl/Tk which uses likelihood calculations and simulations to perform parentage studies with dominant, codominant and cytoplasmic markers. | ||
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* [[Anchor(ITK)]][http://www.itk.org/ Insight Toolkit (ITK)] - an open-source software toolkit for performing registration and segmentation. Created to support the [http://www.nlm.nih.gov/research/visible/visible_human.html Visible Human Project ]. | * [[Anchor(ITK)]][http://www.itk.org/ Insight Toolkit (ITK)] - an open-source software toolkit for performing registration and segmentation. Created to support the [http://www.nlm.nih.gov/research/visible/visible_human.html Visible Human Project ]. | ||
| − | + | ** [http://www.cs.mu.oz.au/~gavinb/projects/itk.php unofficial debian packages ] | |
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=== Unofficial Biology packages === | === Unofficial Biology packages === | ||
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=== Web Based Biology tools === | === Web Based Biology tools === | ||
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=== Links === | === Links === | ||
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[[UbuntuHelp:UbuntuScience]] | [[UbuntuHelp:UbuntuScience]] | ||
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---- | ---- | ||
[[category:CategoryScience]] | [[category:CategoryScience]] | ||
[[category:UbuntuHelp]] | [[category:UbuntuHelp]] | ||
2007年11月30日 (五) 21:54的版本
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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
- a collection of Perl modules that are useful for programmers in bioinformatics/biology
- Clustalw
- This program performs an alignment of multiple nucleotide or amino acid sequences. Clustalx is a gui front end for clustalw. - 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 - A sequence editor with multiple alignment (via CLustalW) and other capabilities
- Phylip - A Package of programs for inferring phylogenies.
- Tree View X - 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 - TREE-PUZZLE is a computer program to reconstruct phylogenetic trees from molecular sequence data by maximum likelihood.
- DIALIGN2 - a command line tool to perform multiple alignment of protein or DNA sequences.
Other Biology software not in Ubuntu
- Bioconductor - bioinformatics tools.
- Emboss - a suite of bioinformatics tools.
- SciCraft - Addon to Octave, clones Simulink. Still in developement, 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 Populationg 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) - an open-source software toolkit for performing registration and segmentation. Created to support the Visible Human Project .
