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'''cufflinks''' [http://cufflinks.cbcb.umd.edu/] Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples | '''cufflinks''' [http://cufflinks.cbcb.umd.edu/] Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples | ||
''' | '''trinityrnaseq''' [http://trinityrnaseq.sourceforge.net/] Novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data | ||
'''velvet''' [http://www.ebi.ac.uk/~zerbino/velvet/] Sequence assembler for very short reads | |||
'''denovo2''' | |||
'''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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'''hmmer''' [http://hmmer.janelia.org/] Biosequence analysis using profile HMM | '''hmmer''' [http://hmmer.janelia.org/] Biosequence analysis using profile HMM | ||
'''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 | ||
'''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 | ||
'''njplot''' [http://pbil.univ-lyon1.fr/software/njplot.html] NJplot is a tree drawing program | '''njplot''' [http://pbil.univ-lyon1.fr/software/njplot.html] NJplot is a tree drawing program | ||
'''paup''' [http://paup.csit.fsu.edu/] Tools for inferring and interpreting phylogenetic trees | '''paup''' [http://paup.csit.fsu.edu/] Tools for inferring and interpreting phylogenetic trees | ||
'''phylip''' [http://evolution.genetics.washington.edu/phylip.html] A package of programs for inferring phylogenies (evolutionary trees) | '''phylip''' [http://evolution.genetics.washington.edu/phylip.html] A package of programs for inferring phylogenies (evolutionary trees) | ||
'''phyml''' [http://www.atgc-montpellier.fr/phyml/] PhyML is a phylogeny software based on the maximum-likelihood principle | '''phyml''' [http://www.atgc-montpellier.fr/phyml/] PhyML is a phylogeny software based on the maximum-likelihood principle | ||
'''tree-puzzle''' [http://www.tree-puzzle.de/] Program to reconstruct phylogenetic trees from molecular sequence data by maximum likelihood | '''tree-puzzle''' [http://www.tree-puzzle.de/] 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) | *インストール済みソフトウェア(その他) |
2012年6月1日 (金) 07:52時点における版
- インストール済みソフトウェア(分子生物学)
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
dbget DBGET is an integrated database retrieval system for major biological databases
EMBOSS [2] EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology
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
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
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
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