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

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

マルチプルアラインメント

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

アセンブラー

CAP3 [7] Multiple Sequence Alignment
TGICL [8] Multiple Sequence Alignment (for huge data set)

Phred [9] 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 [10] SAM Tools provide various utilities for manipulating alignments in the SAM format

bamtools [11] Bamtools is a toolkit for analyzing and managing BAM files

bwa [12] Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence

soap [13] Short Oligonucleotide Analysis Package

bowtie [14] Bowtie is an ultrafast, memory-efficient short read aligner
tophat [15] TopHat is a fast splice junction mapper for RNA-Seq reads
cufflinks [16] Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples

trinityrnaseq [17] 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 [18] Sequence assembler for very short reads

abyss [19] Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler

allpaths-lg [20] The new short read genome assembler

denovo2

遺伝子領域予測

genemark [21] A family of gene prediction programs

genscan [22] Gene prediction

glimmer [23] Glimmer is a system for finding genes in microbial DNA

モチーフ検索

hmmer [24] Biosequence analysis using profile HMM

meme [25] Multiple Em for Motif Elicitation

系統樹解析

mrbayes [26] MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models

njplot [27] NJplot is a tree drawing program

paup [28] Tools for inferring and interpreting phylogenetic trees

phylip [29] A package of programs for inferring phylogenies (evolutionary trees)

phyml [30] PhyML is a phylogeny software based on the maximum-likelihood principle

tree-puzzle [31] 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

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