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==次世代シーケンサデータ解析用== | ==次世代シーケンサデータ解析用== | ||
'''samtools''' [http://samtools.sourceforge.net/] SAM Tools provide various utilities for manipulating alignments in the SAM format | '''samtools''' [http://samtools.sourceforge.net/] SAM Tools provide various utilities for manipulating alignments in the SAM format | ||
'''bamtools''' [https://github.com/pezmaster31/bamtools] Bamtools is a toolkit for analyzing and managing BAM files | |||
'''bwa''' [http://bio-bwa.sourceforge.net/] Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence | '''bwa''' [http://bio-bwa.sourceforge.net/] Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence | ||
'''soap''' [http://soap.genomics.org.cn/index.html] Short Oligonucleotide Analysis Package | '''soap''' [http://soap.genomics.org.cn/index.html] Short Oligonucleotide Analysis Package | ||
'''bowtie''' [http://bowtie-bio.sourceforge.net/index.shtml] Bowtie is an ultrafast, memory-efficient short read aligner | '''bowtie''' [http://bowtie-bio.sourceforge.net/index.shtml] Bowtie is an ultrafast, memory-efficient short read aligner | ||
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'''velvet''' [http://www.ebi.ac.uk/~zerbino/velvet/] Sequence assembler for very short reads | '''velvet''' [http://www.ebi.ac.uk/~zerbino/velvet/] Sequence assembler for very short reads | ||
'''denovo2''' | '''abyss''' [http://www.bcgsc.ca/platform/bioinfo/software/abyss] Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler | ||
'''allpaths-lg''' [http://www.broadinstitute.org/software/allpaths-lg/blog/] The new short read genome assembler | |||
'''denovo2''' | |||
==遺伝子領域予測== | ==遺伝子領域予測== | ||
'''genemark''' [http://exon.gatech.edu/] A family of gene prediction programs | '''genemark''' [http://exon.gatech.edu/] A family of gene prediction programs |
2014年11月25日 (火) 08:06時点における版
ホモロジー検索等
blast Sequence Similarity Search blast+ fasta
blat [1] BLAT on DNA is designed to quickly find sequences of 95% and greater similarity of length 25 bases or more
遺伝子情報取得
dbget DBGET is an integrated database retrieval system for major biological databases
分子生物学用ソフトウェアパッケージ
EMBOSS [2] EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology
マルチプルアラインメント
clustalw Multiple Sequence Alignment clustalw2
muscle [3] Multiple Sequence Alignment faster and more accurate than clustalw
mafft [4] MAFFT is a multiple sequence alignment program
t_coffee [5] Multiple sequence alignment package
Gblocks [6] eliminates poorly aligned positions and divergent regions of an alignment of DNA or protein sequences
アセンブラー
CAP3 [7] Multiple Sequence Alignment TGICL [8] Multiple Sequence Alignment (for huge data set)
Phred [9] The phred software reads DNA sequencing trace files, calls bases, and assigns a quality value to each called base
Phrap Phrap is a program for assembling shotgun DNA sequence data
consed Assembly Editor
次世代シーケンサデータ解析用
samtools [10] SAM Tools provide various utilities for manipulating alignments in the SAM format
bamtools [11] Bamtools is a toolkit for analyzing and managing BAM files
bwa [12] Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence
soap [13] Short Oligonucleotide Analysis Package
bowtie [14] Bowtie is an ultrafast, memory-efficient short read aligner tophat [15] TopHat is a fast splice junction mapper for RNA-Seq reads cufflinks [16] Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples
trinityrnaseq [17] Novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data
velvet [18] Sequence assembler for very short reads
abyss [19] Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler
allpaths-lg [20] The new short read genome assembler
denovo2
遺伝子領域予測
genemark [21] A family of gene prediction programs
genscan [22] Gene prediction
glimmer [23] Glimmer is a system for finding genes in microbial DNA
モチーフ検索
hmmer [24] Biosequence analysis using profile HMM
meme [25] Multiple Em for Motif Elicitation
系統樹解析
mrbayes [26] MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models
njplot [27] NJplot is a tree drawing program
paup [28] Tools for inferring and interpreting phylogenetic trees
phylip [29] A package of programs for inferring phylogenies (evolutionary trees)
phyml [30] PhyML is a phylogeny software based on the maximum-likelihood principle
tree-puzzle [31] Program to reconstruct phylogenetic trees from molecular sequence data by maximum likelihood
lastz
- インストール済みソフトウェア(その他)
Gene Spring (端末室 Windowsマシン上 所内のみ利用可) MATLAB (同上) MATLAB Distributed Computing Server
- 他一般ソフトウェア、プログラム言語
csh tcsh zsh bash perl ruby python gcc icc (Intel Compiler) mpicc