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+
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
TGICL

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

samtools [23] SAM Tools provide various utilities for manipulating alignments in the SAM format

soap [24] Short Oligonucleotide Analysis Package

t_coffee [25]  Multiple sequence alignment package

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