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'''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 | ||
'''CAP3''' | '''CAP3''' Multiple Sequence Alignment | ||
'''clustalw''' | '''clustalw''' Multiple Sequence Alignment | ||
'''clustalw2''' | '''clustalw2''' | ||
'''consed''' | '''consed''' Assembly Editor | ||
'''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 | ||
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'''EMBOSS''' [http://emboss.sourceforge.net/] EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology | '''EMBOSS''' [http://emboss.sourceforge.net/] EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology | ||
'''fasta''' | '''fasta''' Sequence Similarity Search | ||
'''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 | ||
genemark | '''genemark''' [http://exon.gatech.edu/] A family of gene prediction programs | ||
glimmer | '''genscan''' [http://genes.mit.edu/GENSCANinfo.html] Gene prediction | ||
hmmer | |||
'''glimmer''' [http://www.cbcb.umd.edu/software/glimmer/] Glimmer is a system for finding genes in microbial DNA | |||
'''hmmer''' [http://hmmer.janelia.org/] Biosequence analysis using profile HMM | |||
IGV | IGV | ||
lastz | lastz | ||
2012年6月1日 (金) 01:51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）
abyss [1] Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler
allpaths-lg [2] The new short read genome assembler
blast Sequence Similarity Search blast+
blat [3] BLAT on DNA is designed to quickly find sequences of 95% and greater similarity of length 25 bases or more
bowtie [4] Bowtie is an ultrafast, memory-efficient short read aligner
bwa [5] Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence
CAP3 Multiple Sequence Alignment
clustalw Multiple Sequence Alignment clustalw2
consed Assembly Editor
cufflinks [6] Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples
dbget DBGET is an integrated database retrieval system for major biological databases
denovo2
EMBOSS [7] EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology
fasta Sequence Similarity Search
Gblocks [8] eliminates poorly aligned positions and divergent regions of an alignment of DNA or protein sequences genemark [9] A family of gene prediction programs
genscan [10] Gene prediction
glimmer [11] Glimmer is a system for finding genes in microbial DNA
hmmer [12] Biosequence analysis using profile HMM
IGV lastz mafft meme mrbayes muscle njplot paup Phred+Phrap phylip phyml raxml readseq samtools soap sparsehash-1.11 stacks stacks-0.996 t_coffee tgicl_linux tophat tree-puzzle trinityrnaseq velvet
- 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