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'''Gblocks''' [http://molevol.cmima.csic.es/castresana/Gblocks.html] eliminates poorly aligned positions and divergent regions of an alignment of DNA or protein sequences | '''Gblocks''' [http://molevol.cmima.csic.es/castresana/Gblocks.html] eliminates poorly aligned positions and divergent regions of an alignment of DNA or protein sequences | ||
==アセンブラー== | ==アセンブラー== | ||
'''CAP3''' Multiple Sequence Alignment | '''CAP3''' [http://genome.cshlp.org/content/9/9/868.long] Multiple Sequence Alignment | ||
'''TGICL''' | '''TGICL''' | ||
2014年11月25日 (火) 07:52時点における版
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
Phred [8] 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 [9] SAM Tools provide various utilities for manipulating alignments in the SAM format
bwa [10] Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence
soap [11] Short Oligonucleotide Analysis Package
abyss [12] Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler
allpaths-lg [13] The new short read genome assembler
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
velvet [18] Sequence assembler for very short reads
denovo2
遺伝子領域予測
genemark [19] A family of gene prediction programs
genscan [20] Gene prediction
glimmer [21] Glimmer is a system for finding genes in microbial DNA
モチーフ検索
hmmer [22] Biosequence analysis using profile HMM
meme [23] Multiple Em for Motif Elicitation
系統樹解析
mrbayes [24] MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models
njplot [25] NJplot is a tree drawing program
paup [26] Tools for inferring and interpreting phylogenetic trees
phylip [27] A package of programs for inferring phylogenies (evolutionary trees)
phyml [28] PhyML is a phylogeny software based on the maximum-likelihood principle
tree-puzzle [29] 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