ソフトウェア

ホモロジー検索等

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

ペアワイズアライメント

lastz [2] A tool for (1) aligning two DNA sequences, and (2) inferring appropriate scoring parameters automatically

マルチプルアライメント

clustalw　Multiple Sequence Alignment
clustalw2

muscle [3] Multiple Sequence Alignment faster and more accurate than clustalw

mafft [4] MAFFT is a multiple sequence alignment program

t_coffee [5]  Multiple sequence alignment package

Gblocks  [6] eliminates poorly aligned positions and divergent regions of an alignment of DNA or protein sequences

遺伝子情報取得

dbget　DBGET is an integrated database retrieval system for major biological databases

分子生物学用ソフトウェアパッケージ

EMBOSS [7] EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology

アセンブラー

CAP3 [8] Multiple Sequence Alignment
TGICL [9] Multiple Sequence Alignment (for huge data set)

Phred [10] 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

次世代シーケンサデータ解析用

samtools [11] SAM Tools provide various utilities for manipulating alignments in the SAM format

bamtools [12] Bamtools is a toolkit for analyzing and managing BAM files

BEDtools [13] Bedtools utilities are a tools for a wide-range of genomics analysis tasks

bwa [14] Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence

soap [15] Short Oligonucleotide Analysis Package

bowtie [16] Bowtie is an ultrafast, memory-efficient short read aligner
tophat [17] TopHat is a fast splice junction mapper for RNA-Seq reads
cufflinks [18] Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples

trinityrnaseq [19] Novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data

次世代シーケンサデータ解析用：アセンブラー

velvet [20] Sequence assembler for very short reads

abyss [21] Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler

allpaths-lg [22]  The new short read genome assembler

遺伝子領域予測

genemark [23] A family of gene prediction programs

genscan [24] Gene prediction

glimmer [25] Glimmer is a system for finding genes in microbial DNA

augustus [26] AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences

モチーフ検索

hmmer [27] Biosequence analysis using profile HMM

meme [28] Multiple Em for Motif Elicitation

系統樹解析

mrbayes [29] MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models

njplot [30] NJplot is a tree drawing program

paup [31] Tools for inferring and interpreting phylogenetic trees

phylip [32] A package of programs for inferring phylogenies (evolutionary trees)

phyml [33] PhyML is a phylogeny software based on the maximum-likelihood principle

tree-puzzle [34] Program to reconstruct phylogenetic trees from molecular sequence data by maximum likelihood

• 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

• 他一般ソフトウェア、プログラム言語

csh
tcsh
zsh
bash
perl
ruby
python
gcc
icc 　(Intel Compiler)
mpicc