The Thunder Cluster has the Bio Roll installed, which includes many commonly used biology software. To check the complete list, check the Bio Roll documentation

 ABySS  1.3.7  short read genome assembler
 AMOS 3.1.0  
 BEAST 1.8.0  Bayesian MCMC analyses of molecular sequences
 BEAST2 2.1.0  Bayesian MCMC analyses of molecular sequences
 Blast2GO 2.5.0  tools for functional annotation and analysis
 Bowtie  1.0.0  short read aligner
 Bowtie2  2.1.0  short read aligner
 BUCKy 1.4.2  Bayesian concordance analysis for multiple loci
 BWA  0.7.4  low divergency mapper against large genomes
 CAP3 VersionDate 12/21/07  (old) sequence assembler
 CD-HIT 4.6  clustering DNA/protein sequences
 Cufflinks 2.1.1  transcript assembly, abundance, and differential expression in RNA-Seq
 CUSHAW3 3.0.2  gapped short-read aligner
 cutadapt 1.3  removes adapter sequences from reads
 Dindel 1.01  detection of small indels from BAM files
 FastQC 0.10.1  quality control for high througput sequence data
 FASTX-Toolkit 0.0.14  FASTA / FASTQ preprocessing
 FLASh 1.2.8  paired-ends reads merger
 FSA 1.15.8  probabilistic multiple sequence alignment
 GenomeTools 1.5.1  large collection of bioinformatic tools
 Gblocks 0.91b  removes poorly aligned and divergent regions of a DNA or protein alignment
 HyPhy 2.2  hypothesis testing using phylogenies
 MAFFT 7.130  multiple sequece aligner
 MIRA 4.0  hybrid genome & transcriptome assembler and more
 MrBayes 3.2.2  Bayesian phylogenetic inference
 MUMmer 3.23  whole genome aligner
 MUSCLE 3.8.31  multiple sequece aligner
 Oases 0.2.08  de novo transcriptome assembler
 PAML 4.7a  phylogeneti analysis by maximum likelihood, tests of selection
 PEAR 0.9.0  pair-end read merger
 PhyloBayes 3.3f  phylogenetic reconstruction using infinite mixtures
 PhyloBayes-MPI 1.5a  phylogenetic reconstruction using infinite mixtures
 PhyML 20120412 + patch 20131112  maximum likelihood phylogenies from sequence alignments
 Picard 1.107  Java-based command-line utilities to manipulate SAM files
 PLINK 1.07  whole genome association analysis toolset
 PRINSEQ 0.20.4  quality control and data preprocesing
 ProtTest 3.4  aminoacid replacement model selection
 R & Bioconductor 3.0.1 & 2.13  statistical framework & analysis of high-throughput genomic data
 RAxML 8.0.5  maximim-likelihood-based phylogenetic inference
 RSEM 1.2.10  RNA-seq gene expression estimation
 SAMtools 0.1.9  utilities to manipulate SAM and BAM files
 SOAPdenovo2 2.04 r240  de novo short read genome assembler
 Stacks 1.12  builds loci from short reads
 Stampy 1.0.23  
 TopHat 2.0.10  splice junction mapper for RNA-Seq reads
 Trans-ABySS 1.4.8  pipeline for analyzing ABySS-assembled contigs from transcriptomes
 TransDecoder rel16JAN2014  identifies candidate coding regions within transcript sequences
 trimAl 1.2rev59  automated alignment trimming
 Trinity r20131110  de novo transcriptome assembly
 VarScan 2.3.6  variant detection in parallel sequencing data
 Velvet 1.2.10  short read genome assembler
 VEP  74 determine effect of variants on genes, transcripts, proteins, and regulatory regions


Bioinformatics, integrative and System Biology

Center for Molecular Biology and Genetic Engineering 

Av. Cândido Rondon, 400. Campinas - SP

CEP: 13083-875

PO Box 6010

Phone: (+55 19) 3521-1130/1131

Fax: (+55 19) 3521-1089

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