「ソフトウェア」の版間の差分
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'''Gblocks''' [http://molevol.cmima.csic.es/castresana/Gblocks.html] eliminates poorly aligned positions and divergent regions of an alignment of DNA or protein sequences | '''Gblocks''' [http://molevol.cmima.csic.es/castresana/Gblocks.html] eliminates poorly aligned positions and divergent regions of an alignment of DNA or protein sequences | ||
==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 | ||
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'''denovo2''' | '''denovo2''' | ||
==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 | ||
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'''meme''' [http://meme.sdsc.edu/meme/cgi-bin/meme.cgi] Multiple Em for Motif Elicitation | '''meme''' [http://meme.sdsc.edu/meme/cgi-bin/meme.cgi] Multiple Em for Motif Elicitation | ||
==系統樹解析== | |||
'''mrbayes''' [http://mrbayes.sourceforge.net/] MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models | '''mrbayes''' [http://mrbayes.sourceforge.net/] MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models | ||
2012年6月4日 (月) 04:54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
CAP3 Multiple Sequence Alignment TGICL
clustalw Multiple Sequence Alignment clustalw2
muscle [3] Multiple Sequence Alignment faster and more accurate than clustalw
Phred [4] 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
mafft [5] MAFFT is a multiple sequence alignment program
t_coffee [6] Multiple sequence alignment package
Gblocks [7] eliminates poorly aligned positions and divergent regions of an alignment of DNA or protein sequences
次世代シーケンサデータ解析用
samtools [8] SAM Tools provide various utilities for manipulating alignments in the SAM format
bwa [9] Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence
soap [10] Short Oligonucleotide Analysis Package
abyss [11] Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler
allpaths-lg [12] The new short read genome assembler
bowtie [13] Bowtie is an ultrafast, memory-efficient short read aligner tophat [14] TopHat is a fast splice junction mapper for RNA-Seq reads cufflinks [15] Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples
trinityrnaseq [16] Novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data
velvet [17] Sequence assembler for very short reads
denovo2
遺伝子領域予測
genemark [18] A family of gene prediction programs
genscan [19] Gene prediction
glimmer [20] Glimmer is a system for finding genes in microbial DNA
hmmer [21] Biosequence analysis using profile HMM
meme [22] Multiple Em for Motif Elicitation
系統樹解析
mrbayes [23] MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models
njplot [24] NJplot is a tree drawing program
paup [25] Tools for inferring and interpreting phylogenetic trees
phylip [26] A package of programs for inferring phylogenies (evolutionary trees)
phyml [27] PhyML is a phylogeny software based on the maximum-likelihood principle
tree-puzzle [28] 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 Pipeline Pilot
- 他一般ソフトウェア、プログラム言語
csh tcsh zsh bash perl ruby python gcc gcc ver.4 icc (Intel Compiler) mpicc