bio-linux软件包教程,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