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'''consed''' Assembly Editor | '''consed''' Assembly Editor | ||
'''mafft''' [http://mafft.cbrc.jp/alignment/software/] MAFFT is a multiple sequence alignment program | |||
'''t_coffee''' [http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html] Multiple sequence alignment package | |||
'''Gblocks''' [http://molevol.cmima.csic.es/castresana/Gblocks.html] eliminates poorly aligned positions and divergent regions of an alignment of DNA or protein sequences | |||
''' | '''samtools''' [http://samtools.sourceforge.net/] SAM Tools provide various utilities for manipulating alignments in the SAM format | ||
''' | '''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 | ||
'''soap''' [http://soap.genomics.org.cn/index.html] Short Oligonucleotide Analysis Package | |||
'''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 | ||
'''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 | ||
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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 | ||
''' | '''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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'''lastz''' | '''lastz''' | ||
'''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 | ||
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'''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 | ||
2012年6月1日 (金) 07:50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
denovo2
genemark [16] A family of gene prediction programs
genscan [17] Gene prediction
glimmer [18] Glimmer is a system for finding genes in microbial DNA
hmmer [19] Biosequence analysis using profile HMM
lastz
meme [20] Multiple Em for Motif Elicitation
mrbayes [21] MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models
njplot [22] NJplot is a tree drawing program
paup [23] Tools for inferring and interpreting phylogenetic trees
phylip [24] A package of programs for inferring phylogenies (evolutionary trees)
phyml [25] PhyML is a phylogeny software based on the maximum-likelihood principle
tree-puzzle [26] Program to reconstruct phylogenetic trees from molecular sequence data by maximum likelihood
trinityrnaseq [27] Novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data
velvet [28] Sequence assembler for very short reads
- 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