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'''hmmer''' [http://hmmer.janelia.org/] Biosequence analysis using profile HMM | '''hmmer''' [http://hmmer.janelia.org/] Biosequence analysis using profile HMM | ||
'''lastz''' | |||
mafft | '''mafft''' [http://mafft.cbrc.jp/alignment/software/] MAFFT is a multiple sequence alignment program | ||
meme | |||
mrbayes | '''meme''' [http://meme.sdsc.edu/meme/cgi-bin/meme.cgi] Multiple Em for Motif Elicitation | ||
muscle | |||
njplot | '''mrbayes''' [http://mrbayes.sourceforge.net/] MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models | ||
'''muscle''' [http://www.drive5.com/muscle/] Multiple Sequence Alignment faster and more accurate than clustalw | |||
'''njplot''' [http://pbil.univ-lyon1.fr/software/njplot.html] NJplot is a tree drawing program | |||
paup | paup | ||
Phred+Phrap | Phred+Phrap | ||
2012年6月1日 (金) 01:58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
lastz
mafft [13] MAFFT is a multiple sequence alignment program
meme [14] Multiple Em for Motif Elicitation
mrbayes [15] MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models
muscle [16] Multiple Sequence Alignment faster and more accurate than clustalw
njplot [17] NJplot is a tree drawing program
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