ソフトウェア

• 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