ソフトウェア
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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
MUMmer [3] 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
muscle [4] Multiple Sequence Alignment faster and more accurate than clustalw
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
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 [8] 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 [9] Multiple Sequence Alignment TGICL [10] Multiple Sequence Alignment (for huge data set)
Phred [11] 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 [12] SAM Tools provide various utilities for manipulating alignments in the SAM format
bamtools [13] Bamtools is a toolkit for analyzing and managing BAM files
BEDtools [14] Bedtools utilities are a tools for a wide-range of genomics analysis tasks
bwa [15] Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence
soap [16] Short Oligonucleotide Analysis Package
bowtie [17] Bowtie is an ultrafast, memory-efficient short read aligner tophat [18] TopHat is a fast splice junction mapper for RNA-Seq reads cufflinks [19] Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples
trinityrnaseq [20] 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 [21] Sequence assembler for very short reads
abyss [22] Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler
allpaths-lg [23] The new short read genome assembler
遺伝子領域予測
genemark [24] A family of gene prediction programs
genscan [25] Gene prediction
glimmer [26] Glimmer is a system for finding genes in microbial DNA
augustus [27] AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences
モチーフ検索
hmmer [28] Biosequence analysis using profile HMM
meme [29] Multiple Em for Motif Elicitation
系統樹解析
mrbayes [30] MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models
njplot [31] NJplot is a tree drawing program
paup [32] Tools for inferring and interpreting phylogenetic trees
phylip [33] A package of programs for inferring phylogenies (evolutionary trees)
phyml [34] PhyML is a phylogeny software based on the maximum-likelihood principle
tree-puzzle [35] 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