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'''phyml''' [http://www.atgc-montpellier.fr/phyml/] PhyML is a phylogeny software based on the maximum-likelihood principle | '''phyml''' [http://www.atgc-montpellier.fr/phyml/] PhyML is a phylogeny software based on the maximum-likelihood principle | ||
'''samtools''' [http://samtools.sourceforge.net/] SAM Tools provide various utilities for manipulating alignments in the SAM format | |||
'''soap''' [http://soap.genomics.org.cn/index.html] Short Oligonucleotide Analysis Package | |||
'''t_coffee''' [http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html] Multiple sequence alignment package | |||
'''tree-puzzle''' [http://www.tree-puzzle.de/] Program to reconstruct phylogenetic trees from molecular sequence data by maximum likelihood | |||
'''trinityrnaseq''' [http://trinityrnaseq.sourceforge.net/] Novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data | |||
'''velvet''' [http://www.ebi.ac.uk/~zerbino/velvet/] Sequence assembler for very short reads | |||
*インストール済みソフトウェア(その他) | *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) | Gene Spring (端末室 Windowsマシン上 所内のみ利用可) |
2012年6月1日 (金) 02:43時点における版
- インストール済みソフトウェア(分子生物学)
abyss [1] Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler
allpaths-lg [2] The new short read genome assembler
blast Sequence Similarity Search blast+ fasta
blat [3] BLAT on DNA is designed to quickly find sequences of 95% and greater similarity of length 25 bases or more
bowtie [4] Bowtie is an ultrafast, memory-efficient short read aligner tophat [5] TopHat is a fast splice junction mapper for RNA-Seq reads cufflinks [6] Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples
bwa [7] Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence
CAP3 Multiple Sequence Alignment TGICL
clustalw Multiple Sequence Alignment clustalw2
dbget DBGET is an integrated database retrieval system for major biological databases
denovo2
EMBOSS [8] EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology
Gblocks [9] eliminates poorly aligned positions and divergent regions of an alignment of DNA or protein sequences
genemark [10] A family of gene prediction programs
genscan [11] Gene prediction
glimmer [12] Glimmer is a system for finding genes in microbial DNA
hmmer [13] Biosequence analysis using profile HMM
lastz
mafft [14] MAFFT is a multiple sequence alignment program
meme [15] Multiple Em for Motif Elicitation
mrbayes [16] MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models
muscle [17] Multiple Sequence Alignment faster and more accurate than clustalw
njplot [18] NJplot is a tree drawing program
paup [19] Tools for inferring and interpreting phylogenetic trees
Phred [20] 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
phylip [21] A package of programs for inferring phylogenies (evolutionary trees)
phyml [22] PhyML is a phylogeny software based on the maximum-likelihood principle samtools [23] SAM Tools provide various utilities for manipulating alignments in the SAM format
soap [24] Short Oligonucleotide Analysis Package
t_coffee [25] Multiple sequence alignment package
tree-puzzle [26] Program to reconstruct phylogenetic trees from molecular sequence data by maximum likelihood
trinityrnaseq [27] Novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data
velvet [28] Sequence assembler for very short reads
- 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 Pipeline Pilot
- 他一般ソフトウェア、プログラム言語
csh tcsh zsh bash perl ruby python gcc gcc ver.4 icc