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）

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

trinityrnaseq [16] Novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data

velvet [17] Sequence assembler for very short reads

denovo2 

genemark [18] A family of gene prediction programs

genscan [19] Gene prediction

glimmer [20] Glimmer is a system for finding genes in microbial DNA

hmmer [21] Biosequence analysis using profile HMM

meme [22] Multiple Em for Motif Elicitation

mrbayes [23] MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models

njplot [24] NJplot is a tree drawing program

paup [25] Tools for inferring and interpreting phylogenetic trees

phylip [26] A package of programs for inferring phylogenies (evolutionary trees)

phyml [27] PhyML is a phylogeny software based on the maximum-likelihood principle

tree-puzzle [28] Program to reconstruct phylogenetic trees from molecular sequence data by maximum likelihood

lastz

• 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