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'''abyss''' [http://www.bcgsc.ca/platform/bioinfo/software/abyss] Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler | '''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 | '''allpaths-lg''' [http://www.broadinstitute.org/software/allpaths-lg/blog/] The new short read genome assembler | ||
'''blast''' | '''blast''' Sequence Similarity Search | ||
'''blast+''' | '''blast+''' | ||
'''blat''' [http://genome.ucsc.edu/cgi-bin/hgBlat?command=start] BLAT on DNA is designed to quickly find sequences of 95% and greater similarity of length 25 bases or more | '''blat''' [http://genome.ucsc.edu/cgi-bin/hgBlat?command=start] BLAT on DNA is designed to quickly find sequences of 95% and greater similarity of length 25 bases or more | ||
'''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 | ||
'''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''' Multiple Sequence Alignment | |||
'''clustalw2''' | |||
clustalw2 | '''consed''' Assembly Editor | ||
consed | '''cufflinks''' [http://cufflinks.cbcb.umd.edu/] Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples | ||
cufflinks | '''dbget''' DBGET is an integrated database retrieval system for major biological databases | ||
dbget | '''denovo2''' | ||
denovo2 | '''EMBOSS''' [http://emboss.sourceforge.net/] EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology | ||
EMBOSS | '''fasta''' Sequence Similarity Search | ||
fasta | '''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 | |||
genemark | genemark | ||
genscanlinux | genscanlinux | ||
2012年6月1日 (金) 01:42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 genscanlinux glimmer hmmer 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