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'''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 | ||
'''tophat''' [http://tophat.cbcb.umd.edu/] TopHat is a fast splice junction mapper for RNA-Seq reads | |||
'''cufflinks''' [http://cufflinks.cbcb.umd.edu/] Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples | |||
'''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 | ||
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'''clustalw''' Multiple Sequence Alignment | '''clustalw''' Multiple Sequence Alignment | ||
'''clustalw2''' | '''clustalw2''' | ||
'''dbget''' DBGET is an integrated database retrieval system for major biological databases | '''dbget''' DBGET is an integrated database retrieval system for major biological databases | ||
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t_coffee | t_coffee | ||
tgicl_linux | tgicl_linux | ||
tree-puzzle | tree-puzzle | ||
trinityrnaseq | trinityrnaseq | ||
2012年6月1日 (金) 02:17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+ fasta
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 tophat [5] TopHat is a fast splice junction mapper for RNA-Seq reads cufflinks [6] Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples
bwa [7] 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
dbget DBGET is an integrated database retrieval system for major biological databases
denovo2
EMBOSS [8] EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology
Gblocks [9] eliminates poorly aligned positions and divergent regions of an alignment of DNA or protein sequences
genemark [10] A family of gene prediction programs
genscan [11] Gene prediction
glimmer [12] Glimmer is a system for finding genes in microbial DNA
hmmer [13] Biosequence analysis using profile HMM
lastz
mafft [14] MAFFT is a multiple sequence alignment program
meme [15] Multiple Em for Motif Elicitation
mrbayes [16] MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models
muscle [17] Multiple Sequence Alignment faster and more accurate than clustalw
njplot [18] NJplot is a tree drawing program
paup [19] Tools for inferring and interpreting phylogenetic trees
Phred [20] 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
phylip [21] A package of programs for inferring phylogenies (evolutionary trees)
phyml [22] PhyML is a phylogeny software based on the maximum-likelihood principle readseq samtools soap sparsehash-1.11 stacks stacks-0.996 t_coffee tgicl_linux 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