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- 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
abyss [5] Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler
allpaths-lg [6] The new short read genome assembler
blat [7] BLAT on DNA is designed to quickly find sequences of 95% and greater similarity of length 25 bases or more
bowtie [8] Bowtie is an ultrafast, memory-efficient short read aligner tophat [9] TopHat is a fast splice junction mapper for RNA-Seq reads cufflinks [10] Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples
bwa [11] Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence
denovo2
Gblocks [12] eliminates poorly aligned positions and divergent regions of an alignment of DNA or protein sequences
genemark [13] A family of gene prediction programs
genscan [14] Gene prediction
glimmer [15] Glimmer is a system for finding genes in microbial DNA
hmmer [16] Biosequence analysis using profile HMM
lastz
mafft [17] MAFFT is a multiple sequence alignment program
meme [18] Multiple Em for Motif Elicitation
mrbayes [19] MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models
njplot [20] NJplot is a tree drawing program
paup [21] Tools for inferring and interpreting phylogenetic trees
phylip [22] A package of programs for inferring phylogenies (evolutionary trees)
phyml [23] PhyML is a phylogeny software based on the maximum-likelihood principle samtools [24] SAM Tools provide various utilities for manipulating alignments in the SAM format
soap [25] Short Oligonucleotide Analysis Package
t_coffee [26] Multiple sequence alignment package
tree-puzzle [27] Program to reconstruct phylogenetic trees from molecular sequence data by maximum likelihood
trinityrnaseq [28] Novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data
velvet [29] 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