bio linux 创建_[转载]biolinux包含软件
Package
Version
Description
中文简介
act
13.2-1
A DNA sequence
comparison viewer based on Artemis
基于Artemis的DN序列可视化比较工具
ampliconnoise
1bl-0
Programs for the
removal of noise from 454 sequenced PCR amplicons
去除454测序PCR扩增噪音序列
arb
1:1bl1-3
Graphical sequence and
data analysis tools.
图形化序列分析工具
archaeopteryx
0.972.beta9M-3
A phylogenetic tree
viewer and editor
进化树查看编辑器
artemis
13.2-6
Free genome viewer and
annotation tool
免费的本地基因组浏览器
assembly-conversion-tools
0.01-10
Conversion tools for
handling 454 assemblies.
454序列拼接转换工具
backups
0.3-6
Bio-Linux 5/6 backup
utilities.
biolinx5/6旧版本支持组件
base-directories
1.0-37
Essential Bio-Linux
configuration files.
生物信息平台重要配置文件
big-blast
1.0.3-4
The big-blast script
for annotation of long sequences
注释长序列的big-blast脚本
biocode
2.3.3-2
Biocode plugin for
Geneious workbench
Geneious
workbech的Biocode插件
biojava
1.7.1-3
Open-source Java
framework for processing biological data.
Java生物信息相关包
blast
1:1bl-7
Rapid searching of
nucleotide and protein databases.
最著名的序列比对软件
blast+
1:1bl1
Blast+ contains new
builds of the popular blast family of programs from the NCBI.
blast的衍生版
bldp-files
1.1-96
Documentation for
bioinformatics software on Bio-Linux.
平台软件说明文档
blixem
3.1.1-3
Interactive browser
for viewing pairwise Blast results.
可查看blast结果的交互式浏览器
cap3
20080520-1
A base calling
system
base calling系统,是将测序的图片结果转换成序列的过程
*我以前用过cap3的软件是做序列拼接的,不知这是标错了,还是另一个软件
catchall
3.0.1-1
Analyze data about
microbial species abundance
分析微生物特种丰度数据
cd-hit
2009-1020-1
a suite of programs
designed to quickly group sequences
序列聚类分组工具箱
cdbfasta
1:20100722bl-3
FASTA file indexing
and retrieval tools
fasta格式序列文件索引和检索工具
chimeraslayer
1:20100429bl-4
chimeric detection
utility for 16S rRNA
16S
rRNA混合结果检测分析工具
clcsequenceviewer
6.4-1
CLC Free Sequence
Viewer
CLC序列查看器
cloudbl-desktop
1.4
Adds useful links to
the remote desktop for Cloud BL
云服务
clustal
1:1bl-7
Installs clustalw and
clustalx for multiple sequence and profile alignments.
cytoscape
1:2.7.0-8
Platform for
visualizing complex-networks and integrating these with attribute
data
著名基因网络分析平台,复杂调控网络、GO分析
dendroscope
1.4.0-5
Interactive viewer for
large phylogenetic trees.
进化树查看器
denoiser
1:0.851-9
Rapid denoising of
pyrosequencing amplicon data: exploiting the rank-abundance
distribution
高通量测序扩增噪音去除
dialign
1:1bl-2
Segment-based multiple
sequence alignment DIALIGN2 is a command line tool to perform
multiple alignment of protein or DNA sequences. It constructs
alignments from gapfree pairs of similar segments of the sequences.
This scoring scheme for alignments is the basic difference between
DIALIGN and other global or local alignment methods. Note that
DIALIGN does not employ any kind of gap penalty. It has been
published by Morgenstern B. in Bioinformatics. 1999
Mar;15(3):211-8.
多序列比对
dotter
3.1-1
Graphical dotplot
program for detailed comparison of two sequences
两序列dotplot图比较
dust
2bl1-2
Repetitive sequence
masker
重复序列识别
embassy-domainatrix
0.1.0+20100115-1
Extra EMBOSS commands
to handle domain classification file
EMBOSS工具集:结构域分类
embassy-domalign
0.1.0+20100115-1
Extra EMBOSS commands
for protein domain alignment
EMBOSS工具集:结构域比对
embassy-domsearch
0.1.0++20100115-1
Extra EMBOSS commands
to search for protein domains
EMBOSS工具集:结构域检索
embassy-phylip
3.69-1
EMBOSS conversions of
the programs in the phylip package
EMBOSS工具集:进化分析
emboss
1:1bl1-1
extensive set of tools
for bioinformatics and biological database management
EMBOSS工具集:数据库管理
emboss-data
6.3.1-3
data files for the
EMBOSS package
EMBOSS工具集:数据文件
emboss-doc
6.3.1-3
documentation for
EMBOSS
EMBOSS工具集:说明文档
emboss-lib
6.3.1-3
EMBOSS Libraries
EMBOSS工具集:库文件
emboss-test
6.3.1-3
test files for the
EMBOSS package
EMBOSS工具集:测试文件
estscan
2.1-12
detects coding regions
of DNA sequences.
检测DNA编码区
exchanger
1.0-5
lets you store,
annotate and share files via an omixed server
数据注释共享服务
fasta
36t2d5-1
Collection of programs
for searching DNA and protein databases.
类似于blast的序列比对
fastdnaml
1:1bl-2
estimates maximum
likelihood phylogenetic trees from nucleotide sequences
进化树分析
fastqc
0.10.1-2
A quality control
application for high throughput sequence data
高通量测序质量控制软件
fasttree
2.1.3-1
Infers
approximately-maximum-likelihood phylogenetic trees
进化树分析
forester
1.92-10
ATV (A Tree Viewer) is
a Java tool for the visualization of annotated phylogenetic
trees.
进化树可视化
gap2caf
0.20100408-2
Handles conversion of
gap format assemblies to caf format.
格式转换gap为caf
geneious
5.5.7-3
Geneious Basic
workbench from Biomatters
综合分析平台
geneious-genbanksubmit
1.3.0-1
GenBank submission for
Geneious workbench
序列提交工具
genquery
2.2.4-3
GenQuery is a set of
Perl libraries for managing SQL query templates and making
web-based query forms.
Perl包,数据库检索
glimmer3
3.02-1
System for finding
genes in microbial DNA.
微生物基因鉴定
handlebar
2.2.2-7
Handlebar is a
database for storing data about barcodes and acessing the data via
a web front-end.
happy
1.2-2
Multipoint QTL Mapping
in Genetically Heterogeneous Animals
多点QTL作图
hmmer
1:1bl-1
HMM methods for
searching databases for multiple sequence alignments
隐马方式的多序列比对
isacreator
1.6.0-1
GUI to import and edit
ISA dataset descriptions.
ISA数据描述导入与编辑
jalview
1:2.7.0-2
a Java multiple
alignment editor
Java多比对编辑器
jemboss
6.3bl1-8
graphical user
interface to EMBOSS
EMBOSS图形界面
jmotu
1.0.6-2
Clusters barcode DNA
sequence data into molecular operational taxonomic units
DNA序列聚类
jprofilegrid
1:1bl-2
Multiple sequence
alignment tool that generates ProfileGrids
keyring
5
Public key package for
the Bio-Linux package repository
Bio-linux软件包
libajax6
6.3.1-3
EMBOSS library for
commands
EMBOSS库
libajax6-dev
6.3.1-3
development files for
libajax
libajax开发文件
libnucleus6
6.3.1-3
EMBOSS library for
molecular sequence analysis
EMBOSS库:分子序列分析
libnucleus6-dev
6.3.1-3
development files for
libnucleus
libnucleus开发文件
lucy
1:1bl-1
Preparation of raw DNA
sequence fragments for sequence assembly.
原始DNA序列处理用于组装
mcl
1:1bl-2
Tools for clustering
protein groups in to protein families.
蛋白家族聚类
mesquite
2.74-3
Software for
evolutionary biology.
mira
1:1bl-2
Assembly and editing
of nucleotide sequences, including 454 and Solexa support
组装和编辑序列,支持NGS新一代测序
mira-3rd-party
1:1bl-1
Provides useful script
for sequence handling
序列处理
mothur
2bl-5
This is a wrapper
package for mothur
mothus相关包
mrbayes
1:2bl-3
Bayesian estimation of
phylogeny
mrbayes-multi
3.1.2-4
Multiprocessor version
of MrBayes
多线程版的MrBayes
msatfinder
2.0.10-1
Microsatellite
Finder
鉴定微卫星
mspcrunch
2.5-1
a BLAST
post-processing filter.
blast结果分析
mummer
1:1bl-1
a system for rapidly
aligning entire genomes.
序列比对
muscle
1:1bl-2
Bio-Linux wrapper for
the Debian Med muscle package
med muscle包
mview
1.51-3
Multiple alignment
viewer for sequence database search results.
序列检索结果的多序列比对浏览器
ncbi-tools-x11
1:1bl-3
NCBI libraries for
biology applications (X-based utilities)
njplot
1:1bl-2
Phylogenetic tree
drawing program.
系统发育树
nrdb
2-1
Generates
quasi-nonredundant protein and nucleotide sequence databases.
产生类似非冗余蛋白和核酸序列数据库
ocount
0.5-1
Oligonucleotide
frequency counter
寡核苷酸频率统计
oligoarray
2.1-11
Computes
oligonucleotides for microarray construction
芯片设计
oligoarrayaux
3.7-1
Free software that is
required for the OligoArray2.1 software.
芯片设计升级版
omegamap
0.5-1
Detects natural
selection and recombination in DNA or RNA sequences.
检测DNA/RNA序列自然选择和重组
paml
1:1bl1
Phylogenetic analysis
for DNA/protein sequences using max. likelihood
最大似然数法的蛋白/核酸系统发生分析
pfaat
1.0.034-7
Sequence alignment
editor designed for protein family analysis.
蛋白家族的多序列比对分析
phylip
1:1bl-2
Tool for inferring
phylogenies.
系统发生分析
phyml
1:1bl-1
Phylogeny software
based on the maximum-likelihood principle.
最大似然数法的系统发生分析
plymouth-theme
7.0
Boot splash for
Bio-Linux 7
开机画面程序
prank
1:1bl1-2
Multiple alignment
software.
prevent-upgrade
0.2
Stop Bio-Linux from
upgrading on release of 12.04 LTS
防自动升级程序(Ubuntu各版本兼容性差异很大,升级会导致很多软件出错)
priam
2005.07-5
Generate
enzyme-specific profiles for metabolic pathyway prediction
产生酶特异性谱用于代谢通路预测
primer3
1:1bl-1
Primer3 picks primers
for PCR reactions.
PCR引物设计
python-cogent
1:1.4.1bl-1
Python-cogent, or
PyCogent, is a python library for genomic biology.
python基因组生物学包
qiime
2:1bl-8
Quantitative insights
into microbial ecology
定量微生物生态
qtlcart
1.17f-2
Map quantitative
traits using a map of molecular markers.
rasmol
1:1bl-1
Molecular genetics
visualisation tool.
分子遗传可视化工具
rbs-finder
1.0-4
A program to find
Ribosomal binding sites.
rRNA结合位点预测
rdp-classifier
2:1bl1-1
A niave Bayesian
classifier for 16S rRNA sequences.
基于贝叶斯算法 的16S
rRNA分类
readseq
1:1bl-3
Read and reformat
biosequences
生物序列格式转换
sampledata
20041011-10
Sample data for
Bio-Linux packages
平台测序数据集
samtools
1:1bl-3
processing sequence
alignments in SAM and BAM formats
SAM/BAM文件转换分析
seaview
1:1bl1-1
Multiple sequence
alignment editor
sequin
1:1bl-0
Transitional package
that provides bio-linux-ncbi-tools-x11
序列提交NCBI客户端
shared
1.1-2
Some shared files used
by Bio-Linux
共享库
splitstree
4.12.6-2
Analysis and
visualisation tool for distance data from biological sequences
远源序列分析
squint
1.02-4
Java-based multiple
alignment program and editor
多序列比对java版
staden
2006.1.7.0+1.11.6-8
A suite of tools for
sequence analysis.
序列分析工具集
stars
1.2a-12
STARS is an
alternative interface to Staden.
staden的用户界面
t-coffee
1:1bl-3
Multiple Sequence
Alignment
多序列比对
tablet
1.12.03.26-1
Graphical viewer for
next gen sequence assemblies and alignments
高通量测序比对结果可视化程序,同Gbrowser
taxinspector
1.0b3-12
Browser for entries in
the NCBI
taxonomy database
tetra
1.0b3-1
tetranucleotide
frequency calculator with GUI
图型界面的核酸频率统计
themes
6.1
Graphics, icons,
wallpaper and a GDM theme for Bio-Linux 6.
主题v6
themes-v5
1.2
Graphics, icons, KDE
splash screen and a GDM theme for Bio-Linux 5.
主题v5
themes-v7
7.0-12
Graphics, icons,
wallpaper and desktop settings for Bio-Linux 7
主题v7
transterm-hp
1:1bl1-1
finds rho-independent
transcription terminators in bacterial genomes
在细胞基因组中,查找rho因子不依赖的转录终止子
tree-puzzle
1:1bl-1
pylogenetic tree
reconstruction from molecular sequence
基于分子序列的系统发生树构建
treeview
1:1bl-1
A simple program for
displaying phylogenies.
系统发生/进化树显示
trnascan
1:1bl1-1
searches for tRNA
genes in genomic sequences.
基因组tRNA预测
tutorials
1-23
Tutorials and
documentation for Bio-Linux users.
帮助文档
unity-lens
0.2
unity lens for
Bio-Linux
搜索滤镜
usb-maker
7.0-1
Script to generate
Bio-Linux live memory sticks.
USB版系统定制程序
wise2
1:1bl1-2
Tool for comparison of
biopolymers, DNA, and protein sequence.
比较生物序列聚合物
xcut
1.4-3
A re-write of the GNU
cut command with many new features.
cut改进版
zsh
1-18
Z-Shell wrapper
package for Bio-Linux.
Z-shell
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