软件包: qiime (1.8.0+dfsg-4ubuntu1)
qiime 的相关链接
Trisquel 的资源:
下载源码包 qiime:
- [qiime_1.8.0+dfsg-4ubuntu1.dsc]
- [qiime_1.8.0+dfsg.orig.tar.xz]
- [qiime_1.8.0+dfsg-4ubuntu1.debian.tar.xz]
维护者:
Original Maintainers:
- Debian Med Packaging Team (Mail Archive)
- Steffen Moeller
- Tim Booth
- Andreas Tille
外部的资源:
- 主页 [www.qiime.org]
相似软件包:
Quantitative Insights Into Microbial Ecology
QIIME (canonically pronounced ‘Chime’) is a pipeline for performing microbial community analysis that integrates many third party tools which have become standard in the field. A standard QIIME analysis begins with sequence data from one or more sequencing platforms, including
* Sanger, * Roche/454, and * Illumina GAIIx.With all the underlying tools installed, of which not all are yet available in Debian (or any other Linux distribution), QIIME can perform
* library de-multiplexing and quality filtering; * denoising with PyroNoise; * OTU and representative set picking with uclust, cdhit, mothur, BLAST, or other tools; * taxonomy assignment with BLAST or the RDP classifier; * sequence alignment with PyNAST, muscle, infernal, or other tools; * phylogeny reconstruction with FastTree, raxml, clearcut, or other tools; * alpha diversity and rarefaction, including visualization of results, using over 20 metrics including Phylogenetic Diversity, chao1, and observed species; * beta diversity and rarefaction, including visualization of results, using over 25 metrics including weighted and unweighted UniFrac, Euclidean distance, and Bray-Curtis; * summarization and visualization of taxonomic composition of samples using pie charts and histogramsand many other features.
QIIME includes parallelization capabilities for many of the computationally intensive steps. By default, these are configured to utilize a mutli-core environment, and are easily configured to run in a cluster environment. QIIME is built in Python using the open-source PyCogent toolkit. It makes extensive use of unit tests, and is highly modular to facilitate custom analyses.
其他与 qiime 有关的软件包
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- dep: fasttree
- phylogenetic trees from alignments of nucleotide or protein sequences
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- dep: king
- interactive system for three-dimensional vector graphics
-
- dep: libc6 (>= 2.15)
- GNU C Library: Shared libraries
同时作为一个虚包由这些包填实: libc6-udeb
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- dep: libffi6 (>= 3.0.4)
- Foreign Function Interface library runtime
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- dep: libgmp10
- Multiprecision arithmetic library
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- dep: libjs-jquery
- JavaScript library for dynamic web applications
-
- dep: pynast (>= 1.2.2)
- alignment of short DNA sequences
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- dep: python (<< 2.8)
- interactive high-level object-oriented language (default version)
- dep: python (>= 2.7)
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- dep: python-biom-format (>= 1.2.0)
- Biological Observation Matrix (BIOM) format (Python 2)
-
- dep: python-cogent (>= 1.5.3)
- framework for genomic biology
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- dep: python-matplotlib
- Python based plotting system in a style similar to Matlab
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- dep: python-numpy
- Numerical Python adds a fast array facility to the Python language
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- dep: python-qcli
- separated module of pyqi needed for QIIME package
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- rec: ampliconnoise
- removal of noise from 454 sequenced PCR amplicons
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- rec: blast2
- transitional dummy package to ncbi-blast+-legacy
- 或者 blast+-legacy
- 软件包暂时不可用
-
- rec: cd-hit
- suite of programs designed to quickly group sequences
-
- rec: chimeraslayer
- detects likely chimeras in PCR amplified DNA
-
- rec: clearcut
- extremely efficient phylogenetic tree reconstruction
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- rec: infernal
- inference of RNA secondary structural alignments
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- rec: muscle
- Multiple alignment program of protein sequences
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- rec: parsinsert
- Parsimonious Insertion of unclassified sequences into phylogenetic trees
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- rec: python-mpi4py
- bindings of the Message Passing Interface (MPI) standard
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- rec: qiime-data
- Quantitative Insights Into Microbial Ecology (supporting data)
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- rec: r-cran-optparse
- GNU/R Command line option parser
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- sug: cytoscape
- 软件包暂时不可用
-
- sug: emperor
- 软件包暂时不可用
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- sug: rdp-classifier
- extensible sequence classifier for fungal lsu, bacterial and archaeal 16s
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- sug: t-coffee
- Multiple Sequence Alignment
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- sug: torque-client
- 软件包暂时不可用