ソフトウェア

ホモロジー検索等

blast [1] Sequence Similarity Search
blast+
fasta

blat [2] 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 [3] A tool for (1) aligning two DNA sequences, and (2) inferring appropriate scoring parameters automatically

MUMmer [4] MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form.

マルチプルアライメント

clustalw  Multiple Sequence Alignment
clustalw2 [5] 
clustal Omega [6] Fast, accurate, scalable multiple sequence alignment for proteins

muscle [7] Multiple Sequence Alignment faster and more accurate than clustalw

mafft [8] MAFFT is a multiple sequence alignment program

t_coffee [9]  Multiple sequence alignment package

Gblocks  [10] Gblocks 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 [11] 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 [12] Multiple Sequence Alignment
TGICL [13] Multiple Sequence Alignment (for huge data set)

Phred [14] 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 [15] SAM Tools provide various utilities for manipulating alignments in the SAM format

bamtools [16] Bamtools is a toolkit for analyzing and managing BAM files

BEDtools [17] Bedtools utilities are a tools for a wide-range of genomics analysis tasks

bwa [18] Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence

soap [19] Short Oligonucleotide Analysis Package

bowtie [20] Bowtie is an ultrafast, memory-efficient short read aligner
tophat [21] TopHat is a fast splice junction mapper for RNA-Seq reads
cufflinks [22] Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples

trinityrnaseq [23] 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 [24] Sequence assembler for very short reads

abyss [25] Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler

allpaths-lg [26]  The new short read genome assembler. Type 「module load allpathslg/version_number」 before use. You can confirm the "newest version number" typing 「ls /bio/package/allpahslg」

遺伝子領域予測

genemark [27] A family of gene prediction programs

genscan [28] Gene prediction

glimmer [29] Glimmer is a system for finding genes in microbial DNA

augustus [30] AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences

モチーフ検索

interproscan [31] A tool that combines different protein signature recognition methods into one resource

hmmer [32] Biosequence analysis using profile HMM

meme [33] Multiple Em for Motif Elicitation

系統樹解析

mrbayes [34] MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models

njplot [35] NJplot is a tree drawing program

paup [36] Tools for inferring and interpreting phylogenetic trees

phylip [37] A package of programs for inferring phylogenies (evolutionary trees)

phyml [38] PhyML is a phylogeny software based on the maximum-likelihood principle

tree-puzzle [39] 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