实用的学习生物技术的软件：生物软件会用这个就够了

Geneious是一款综合性的生物信息学软件，用于分析和处理生物信息学数据，支持序列对比和系统学分析、引物设计、克隆和限制性分析、使用NCBI和EMBL,、BLAST、蛋白质结构查看、自动化医学搜索等功能。

下载安装

下载地址http://geneious.com/download包括Windows, Mac, and Linux版本。需要Java程序的支持。

Geneious主窗口

包括四个界面，来源面板，文件列表，文件视图与帮助面板。

数据来源面板

显示了保存的文件与提供的服务。可以查看自己的文件，进入NCBI（Gene, Genome, Nucleotide, PopSet, Protein, Pubmed, SNP, Structure and Taxonomy等数据库），进入EMBL（UniProt.数据库），共享自己的数据库（需要安装），查看同事的数据库（需要安装）。

文件列表

显示了文件夹内各种类型的文件。点击文件在下面窗口可以看到内容，对类型相似的文件可以多选，共同查看。双击可以查看具体内容。可任意排序、调整。

文件视图

可以查看序列，比对，树，3D结构，文章摘要等。

帮助窗口

会显示实时帮助

工具条

功能条

文件栏

编辑栏

视图栏

工具栏

序列栏

注释、预测栏

帮助栏

导入、输出和查找从硬盘导入序列

输入格式

Format

Extensions

Data types

Common sources

BED

*.bed

Annotations

UCSC

Common Assembly Format

*.caf

Contigs

Sequencher

Clustal

*.aln

Alignments

ClustalX

CSFASTA

*.csfasta

Color space FASTA

ABI SOLiD

DNAStar

*.seq, *.pro

Nucleotide & protein sequences

DNAStar

DNA Strider

*.str

Sequences

DNA Strider (Mac program), ApE

Embl/UniProt

*.embl, *.swp

Sequences

Embl, UniProt

Endnote (8.0 or 9.0) XML

*.xml

Journal article references

Endnote,Journal article websites

FASTA

*.fasta, *.fas, etc.

Sequences, alignments

PAUP*,ClustalX, BLAST, FASTA

FASTQ

*.fastq, *.fasq

Sequences with quality

Solexa/Illumina

GCG

*.seq

Sequences

GCG

GenBank

*.gb, *.xml

Nucleotide & protein sequences

GenBank

Geneious

*.xml, *.geneious

Preferences, databases

Geneious

Geneious Education

*.tutorial.zip

Tutorial, assignment etc.

Geneious

GFF

*.gff

Annotations

Sanger Artemis

MEGA

*.meg

Alignments

MEGA

Molecular structure

*.pdb, *.mol, *.xyz, *.cml,

*.gpr, *.hin, *.nwo

3D molecular structures

3D structure databases and programs

Newick

*.tre, *.tree, etc.

Phylogenetic trees

PHYLIP, Tree-Puzzle, PAUP*, ClustalX

Nexus

*.nxs, *.nex

Trees, Alignments

PAUP*, Mesquite, MrBayes & MacClade

PDB

*.pdb

3D Protein structures

SP3, SP2, SPARKS, Protein Data Bank

PDF

*.pdf

Documents, presentations

Adobe Writer, LATEX, Miktex

Phrap ACE

*.ace

Contig assemblies

Phrap/Consed

PileUp

*.msf

Alignments

pileup (gcg)

PIR/NBRF

*.pir

Sequences, alignments

NBRF PIR

Qual

*.qual

Quality file

Associated with a FASTA file

Raw sequence text

*.seq

Sequences

Any file that contains only a sequence

Rich Sequence Format

*.rsf

Sequences, alignments

GCGs NetFetch

Comma/Tab Separated Values

*.CSV, *.tsv

Spreadsheet files

Microsoft Excel

SAM/BAM

*.sam, *.bam

Contigs

SAMtools

Sequence Chromatograms

*.ab1, *.scf

Raw sequencing trace & sequence

Sequencing machines

VCF

*.VCF

Annotations

1000 Genomes Project

Vector NTI sequence

*.gb, *.gp

Nucleotide & protein sequences

Vector NTI

Vector NTI/AlignX alignment

*.apr

Alignments

Vector NTI, AlignX

Vector NTI Archive

*.ma4, *.pa4, *.oa4,

Nucleotide & protein sequences,

*.ea4, *.ca6

enzyme sets and Publications

Vector NTI

Vector NTI/ContigExpress

*.cep

Nucleotide sequence assemblies

Vector NTI

Vector NTI database

VNTI Database

Nucleotide & protein sequences,

enzyme sets and publications

Vector NTI

从公共数据库导入数据

输出格式有很多

Data type

Export format options

DNA sequence

FASTA, Genbank XML, Genbank flat, Geneious

Amino acid sequence

FASTA, Genbank XML, Genbank flat, Geneious

Chromatogram sequence

ABI, Geneious

Sequence with quality

FastQ, Qual, Geneious

Annotation

GFF, BED, Geneious

Multiple sequence alignment

Phylip, FASTA, NEXUS, MEGA, Geneious

Assembly

Phrap ACE, Geneious, SAM/BAM

Phylogenetic tree

Phylip, FASTA, NEXUS, Newick, MEGA, Geneious

PDF document

PDF, Geneious

Publication

EndNote 8.0, Geneious

Graphs

CSV, WIG

Document Properties

CSV, TSV, Geneious

文件种类包括序列文件、引物文件、酶文件、染色体文件、contig、蛋白序列、发育树、3D结构、序列比对文件、文章、pdf、其他

可以搜索和过滤文件

创建、查看和编辑序列

序列视图

侧控制栏：普通、图像、表格、注释、实时注释和预测、限制性分析、其他、统计

显示核酸、互补链、翻译，可选密码子与蛋白质颜色

可以显示限制性酶切位点

实时统计所选区域的碱基、氨基酸、密码子使用等情况

抬头栏：序列视图、注释、点阵图、文本总结、信息

DNA、RNA、蛋白质结构查看

可以查看RNA、DNA结构

利用注释工作

可以查看，个性化风格、导出表格、

序列比对

可进行双序列、多序列、基因组比对，翻译成蛋白质比对、点阵图

从头拼接、Map到参考序列

建树

引物设计

可以设计引物、克隆引物、遗传分析用的大量引物、批量设计引物、

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