List of Tools Available in MolBioCloud

Fully Installed, Configured, Tested and Documented

(Click the category title to expand or collapse the list)
Name Description
Bamtools Toolkit For Manipulating Bam (Genome Alignment) Files
Big-Blast The Big-Blast Script For Annotation Of Long Sequences
Blast2 Basic Local Alignment Search Tool
Blixem Interactive Browser For Viewing Pairwise Blast Results.
Bowtie Ultrafast Memory-Efficient Short Read Aligner
Bowtie2 Ultrafast Memory-Efficient Short Read Aligner
Bowtie2-Debug Ultrafast Memory-Efficient Short Read Aligner
Bwa Burrows-Wheeler Aligner
Clustalw Multiple sequence Alignment
Clustalx Multiple sequence Alignment
Dialign Segment-Based Multiple Sequence Alignment
Dotter Graphical Dotplot Program For Detailed Comparison Of Two Sequences
Hisat2 Fast And Sensitive Alignment Program For Mapping Next-Generation Sequencing Reads
Jaligner Smith-Waterman Algorithm With GotohS Improvement
Jalview Multiple Alignment Editor
Jprofilegrid Multiple Sequence Alignment Tool That Generates Profilegrids
Lastz Aligns Two Dna Sequences, Inferring Appropriate Parameters Automatically
Maq Maps Short Fixed-Length Polymorphic Dna Sequence Reads To Reference Sequences
Mspcrunch A Blast Post-Processing Filter.
Mummer Efficient Sequence Alignment Of Full Genomes
Muscle Multiple Alignment Program Of Protein Sequences
Mview Multiple Alignment Viewer For Sequence Database Search Results.
Ncbi-Blast+ Next Generation Suite Of Blast Sequence Search Tools
Ncbi-Blast+-Legacy Ncbi Blast Legacy Call Script
Perm Efficient Mapping Of Short Reads With Periodic Spaced Seeds
Pfaat Sequence Alignment Editor Designed For Protein Family Analysis.
Prank Probabilistic Alignment Kit For Dna, Codon And Amino-Acid Sequences
Probcons Probabilistic Consistency-Based Multiple Sequence Alignment
Squint Java-Based Multiple Alignment Program And Editor
T-Coffee Multiple Sequence Alignment
Name Description
Abyss De Novo, Parallel, Sequence Assembler For Short Reads
Assembly-Conversion-Tools Conversion Tools For Handling 454 Assemblies.
Cortex-Con Efficient And Low-Memory Software For Consensus Genome Assembly
Gnx-Tools Basic Genome Assembly Statistic Tool To Calculate Nx Values E.G. N50,N10,Ng50
Libpandaseq-Sam1 Pair-End Read Assembler
Lucy Preparation Of Raw Dna Sequence Fragments For Sequence Assembly
Mira-3Rdparty Additional Useful Tools To Accomapany The Mira Assembler
Mira-Assembler Whole Genome Shotgun And Est Sequence Assembler
Pandaseq Pair-End Read Assembler
Ray Parallel De Novo Genome Assemblies Of Next-Gen Sequencing Data
Ray-Extra Scripts And Xsl Sheets For Post-Processing For Ray De Novo Assembler
Ssake Genomics Application For Assembling Millions Of Very Short Dna Sequences
Velvet Nucleic Acid Sequence Assembler For Very Short Reads
A5-miseq De Novo Assembly & Analysis Of Illumina Sequence Data
Staden Dna Sequence Assembly (Gap4/Gap5), Editing And Analysis Tools
Name Description
Hadoop Distributed Data Processing
Spark Compute Engine For Hadoop Data
Neo4J Graph Engine
OpenRefine Data Science
MongoDB Document-oriented NOSQL database engine
PostgreSQL Relational Database Management System
Name Description
MySQL Sql Database
Taxinspector Browser For Entries In The Ncbi Taxonomy Database
Nrdb Generates Quasi-Nonredundant Protein And Nucleotide Sequence Databases
Name Description
R Gnu R Statistical Computation And Graphics System
Weka Machine Learning Package
H2O Machine Learning Package
Aspera Connect High Speed Data Transfer
RBioconductor R Bioconductor Packages
KNIME Datamining
Name Description
Happy Multipoint Qtl Mapping In Genetically Heterogeneous Animals
Qtlcart Map Quantitative Traits Using A Map Of Molecular Markers.
Plink
Whole genome association analysis
Merlin Whole genome association analysis
Name Description
MetaboMiner Identification of metabolites from 2D NMR
MolFind Identification of compounds from HPLC/MS data
OpenMS Metabolomics analysis platform
Name Description
Axiome Qiime And Mothur Automation Toolkit
Axiome-Dev Qiime Automation Toolkit - Plugin Development
BioBakery Metagenomics Suite
Catchall Analyze Data About Microbial Species Abundance
HUMAaN2 Hmp Unified Metabolic Analysis Network
Jmotu Clusters Barcode Dna Sequence Data Into Molecular Operational Taxonomic Units
Metavelvet Extension Of Velvet Assembler To De Novo Metagenomic Assembly
Microbiomeutil Microbiome Analysis Utilities
Mothur Sequence Analysis Suite For Research On Microbiota
Qiime Quantitative Insights Into Microbial Ecology
MetaPhlAn Metagenomics
Qiime-Default-Reference Qiime Default Reference Dataset
Rdp-Classifier Taxonomic Assignment From Next Generation Sequencing
Sortmerna Tool For Filtering, Mapping And Otu-Picking Ngs Reads
Vsearch Tool For Processing Metagenomic Sequences
Name Description
Cytoscape Platform For Visualizing Complex-Networks And Integrating These With Attribute Data
Khmer K-Mer Counting, Filtering And Graph Traversal
Priam Generate Enzyme-Specific Profiles For Metabolic Pathyway Prediction
Gephi Graph analysis platform
Name Description
Archaeopteryx A Phylogenetic Tree Viewer And Editor
Clearcut Relaxed Neighbor Joining
Dendroscope Interactive Viewer For Large Phylogenetic Trees.
Fastdnaml Tool For Construction Of Phylogenetic Trees Of Dna Sequences
Fasttree Phylogenetic Trees From Alignments Of Nucleotide Or Protein Sequences
MEGAN Phylogenetics Analysis
Mesquite Software For Evolutionary Biology.
Mrbayes-Mpi Bayesian Inference Of Phylogeny - Mpi Version
Njplot Phylogenetic Tree Drawing Program
Omegamap Detects Natural Selection And Recombination In Dna Or Rna Sequences.
Paml Phylogenetic Analysis By Maximum Likelihood (Paml)
Parsinsert Parsimonious Insertion Of Unclassified Sequences Into Phylogenetic Trees
Phylip No Description
Phyml Phylogenetic Estimation Using Maximum Likelihood
Raxml Randomized Axelerated Maximum Likelihood Of Phylogenetic Trees
Tree-Puzzle Reconstruction Of Phylogenetic Trees By Maximum Likelihood
Tree-Puzzle-Doc Reconstruction Of Phylogenetic Trees By Maximum Likelihood
Name Description
TexStudio Text Processing
LibreOffice Office Suite
Inkscape Vector Graphics Editing Tool
GIMP Imaging Editing Tool
Name Description
Bioperl Perl Tools For Computational Molecular Biology
Bioperl-Run Bioperl Wrappers: Scripts
Libbiojava>-Java-Demos Example Programs For Biojava
Anaconda2 Python Programming Environment
Eclipse Integrated Development Environment
iPython Python Development Environment
Scala Bigdata Programming Language
PHP Programming
Perl Programming
Python Programming
Name Description
Biosquid Utilities For Biological Sequence Analysis
Cd-Hit A Suite Of Programs Designed To Quickly Group Sequences
Cdbfasta Constant Database Indexing And Retrieval Tools For Multi-Fasta Files
Chimeraslayer Detects Likely Chimeras In Pcr Amplified Dna
Ea-Utils Command-Line Tools For Processing Biological Sequencing Data
EMBOSS Extra Emboss Commands To Handle Domain Classification File
Estscan2 Detects Coding Regions Of Dna Sequences
Fasta Collection Of Programs For Searching Dna And Protein Databases.
Gap2Caf Handles Conversion Of Gap Format Assemblies To Caf Format.
Glam2 Gapped Protein Motifs From Unaligned Sequences
Glimmer3 Gene Detection In Archea And Bacteria
Hmmer Profile Hidden Markov Models For Protein Sequence Analysis
Hyphy Analysis Of Genetic Sequences Using Multiple Techniques
Jellyfish Count K-Mers In Dna Sequences
Last-Align Genome-Scale Comparison Of Biological Sequences
Mafft Multiple Alignment Program For Amino Acid Or Nucleotide Sequences
Mdust Repetitive Sequence Masker
Meme Search For Common Motifs In Dna Or Protein Sequences
Msatfinder Microsatellite Finder
Ocount Oligonucleotide Frequency Counter
Oligoarray Computes Oligonucleotides For Microarray Construction
Predictprotein Suite Of Protein Sequence Analysis Tools
Primer3 Tool To Design Flanking Oligo Nucleotides For Dna Amplification
Rbs-Finder A Program To Find Ribosomal Binding Sites.
Readseq Conversion Between Sequence Formats
Splitstree Analysis And Visualisation Tool For Distance Data From Biological Sequences
Sputnik-Mononucleotide Searches Dna Sequence Files In Fasta Format For Microsatellite Repeats
Sumatra Fast And Exact Comparison And Clustering Of Sequences
Tetra Tetranucleotide Frequency Calculator With Gui
Transterm-Hp Transterm Finds Rho-Independent Transcription Terminators In Bacterial Genomes.
Transtermhp Find Rho-Independent Transcription Terminators In Bacterial Genomes
Trnascan Trnascan-Se Searches For Trna Genes In Genomic Sequences.
Trnascan-Se Search For Trna Genes In Genomic Sequences
Wise Comparison Of Biopolymers, Commonly Dna And Protein Sequences
Name Description
Omssa Open mass spectrometry search engine
Tandem Spectrum modeller
ProteoWizard Proteomics data analysis
Name Description
Amplicon Noise Programs For The Removal Of Noise From 454 Sequenced Pcr Amplicons
Bcftools Suite Of Utilities For Ngs Data Analysis
Bedtools Suite Of Utilities For Comparing Genomic Features
Berkeley-Express Streaming Quantification For High-Throughput Sequencing
Cap3 A Base Calling System
Fastqc A Quality Control Application For High Throughput Sequence Data
Fastx-Toolkit Fastq/A Short Nucleotide Reads Pre-Processing Tools
Fraggenescan Finds (Fragmented) Genes In Short Reads
FLASH Merge Mates From Fragments That Are Shorter Than Twice The Read Length
Macs14 Model-Based Analysis Of Chip-Seq On Short Reads Sequencers
Pass2 Peak Calling In Chip Data Based On Poisson De-Clumping
Picard-Tools Command Line Tools To Manipulate Sam And Bam Files
Samtools Processing Sequence Alignments In Sam And Bam Formats
padding-bottom:2px;padding-top:2px' Sambamba
Process Your Bam Data Faster
Samblaster A Tool To Mark Duplicates And Extract Discordant And Split Reads From Sam Files
Scythe Bayesian Adapter Trimmer For Nextgen Sequence Reads
Seqprep Tool For Stripping Adaptors And/Or Merging Paired Reads With Overlap
Skewer A Fast And Sensitive Adapter Trimmer For Illumina Paired-End Sequences
Sickle Windowed Adaptive Trimming Tool For Fastq Files Using Quality
Stacks Pipeline For Building Loci From Short-Read Sequences
Stacks-Web Web Interface For Displaying Loci From Short-Read Sequences
WASP Sequencing Bias Identification And Correction
Trace2Dbest Processes Trace Files Into Dbest Submissions
Transdecoder Find Coding Regions Within Transcripts
Swarm Robust And Fast Clustering Method For Amplicon-Based Studies

SNP

Name Description
Beam2 Snp-Snp Interaction Association Mapping Based On Snp-Block Models
Sift Predicts If A Substitution In A Protein Has A Phenotypic Effect
SVDetect Structural Variant Detection
LumpyExpress Variant Calling
Name Description
Infernal Inference Of Rna Secondary Structural Alignments
Pymol Molecular Graphics System
Rasmol Visualize Biological Macromolecules
Name Description
Ncbi-Tools-Bin Ncbi Libraries For Biology Applications (Text-Based Utilities)
Ncbi-Tools-X11 Ncbi Libraries For Biology Applications (X-Based Utilities)
SRA Toolkit Ncbi Sra Toolkit
AWS SDK Cloud Toolkit
UCSC tools Genomics Tools
Name Description
Bitseq Bayesian Inference Of Transcripts From Sequencing Data
Cufflinks Transcript Assembly, Differential Expression And Regulation For Rna-Seq
Cuffdiff Differential Expression
Maxd Maxd Is A Data Warehouse And Visualisation Environment For Genomic Expression Data.
Rsem Rna-Seq By Expectation-Maximization
DaPars Differential Polyadenylation Site Usage Analysis
Asarp Allele Specific Expression Analysis
VirusFusionSeq Virus Integration Identification And Analysis
Tophat Fast Splice Junction Mapper For Rna-Seq Reads
Tophat2 Fast Splice Junction Mapper For Rna-Seq Reads
Trinityrnaseq Rna-Seq De Novo Assembly
Trinityrnaseq-Sampledata Rna-Seq De Novo Assembly
CircExplorer2 Circular Rna Identification And Analysis
Name Description
Artemis Free Genome Viewer And Annotation Tool
Clcsequenceviewer Clc Free Sequence Viewer
Tablet Graphical Viewer For Next Gen Sequence Assemblies And Alignments
Treeviewx Displays And Prints Phylogenetic Trees
Weblogo Create Sequence Logos From Biological Sequence Alignments
gnuplot Command line graphic utility
Name Description
Geneious Geneious Basic Workbench From Biomatters
Jemboss Graphical User Interface To Emboss
RStudio Gui Interface For The R
Ugene Integrated Bioinformatics Toolkit
MySQL workbench Sql Workbench
Galaxy-Server Web-Based Analysis Environment For Bioinformatics

On-Demand, Configured, Tested and Documented

(Click the category title to expand or collapse the list)
Tools/Packages Available for On-Demand Installation
Drug databases
Software tools related to dental practice
Epidemiology related sotware tools
Software tools for Hospital Information Systems
Image processing and visualization tools
Image processing and visualization tools for development
Software tools for medical laboratories
Software tools for oncology
Software tools for pharmaceutical research
Software tools for medical physicists
Software tools for practice management
Software tools for psychology
Software tools for rehabilitation technologies
Software tools for medical research
Tools/Packages Available for On-Demand Installation
chemtoolChemical structures drawing program
garlic A visualization program for biomolecules
pymol Molecular Graphics System
gromacs Molecular dynamics simulator, with building and analysis tools
mopac7 Semi-empirical Quantum Chemistry Library
openbabel Chemical toolbox utilities
Workflows Available for On-Demand Installation
assessing_target_enrichment Workflows to compute coverage on targeted regions when using hybrid-capture
bisulfighter A pipeline for accurate detection of methylated cytosines and differentially methylated regions
blast_top_hit_species Workflow to count species of top nr BLASTX hits of a transcriptome
blockclust_workflow BlockClust Workflow
caddsuite_workflows CADDSuite workflows for use in galaxy
chemicaltoolbox_library_hole_filling_workflow Given one library, it extends all molecules by similar molecules of an other library and thus fill gaps in an automatic manner.
chemicaltoolbox_merging_chemical_databases_workflow Preparation of a large compound library by merging of chemical databases using the chemicaltoolbox.
chipseq_workflows ChIP-seq workflows annotated for use with Refinery Platform
codonlogo Codon based sequence logo generator.
deeptools_workflows A collection of workflows using the deepTools
detrprok_wf ncRNA detection in prokaryote oriented RNAseq
differential_expression_analysis_pipeline_for_rnaseq_data differential_expression_analysis_pipeline_for_rnaseq_data
fastqc_workflow FastQC workflow designed for use with Refinery Platform
find_genes_located_nearby_workflow Galaxy workflow for the identification of candidate genes clusters
find_three_genes_located_nearby_workflow Galaxy workflow for the identification of candidate genes clusters with three known genes
geneseqtofamily Workflow based on the Ensembl GeneTrees pipeline to identify homologous genes and generate gene trees
glimmer Glimmer
glimmer_gene_calling_workflow Gene calling with glimmer and a trainingset of know genes.
interproscan_to_excel Convert interproscan raw or xml output to an Excel file
linkyx Fully automated pipeline for detection of sex linked genes using RNA-Seq data
mdust mdust
metavisitor_workflows A collection of workflows using the Metavisitor tools
mimodd_workflows Some example workflows for use with MiModD
mmuflr MMuFLR: Missense Mutation and Frameshift Location Reporter Workflow
nextgen_variant_identification SNVMix-based tools for variant calling from aligned Illumina sequence data
pcr_markers Tools for design of PCR-based Markers from Variant Data
phephenix Public Health England SNP calling Pipeline
prims_workflows Workflows module of Plant Research International's Mass Spectrometry (PRIMS) solution using a combination of tools from different packages
protein_funcional_analysis_similarities Provides common characteristics among similar proteins.
proteogenomics_splice_junc_search_db Generate Novel Splice Junction Search DBs from RNAseq
proteomics_novel_peptide_filter_workflow Workflow to filter a Proteomics Search DB for novel peptides
proteomics_rnaseq_reduced_db_workflow Workflow to filter a Proteomics Search DB by RNA-seq transcript expression analysis
proteomics_rnaseq_sap_db_workflow Workflow to create Proteomics Search DB from RNA-seq Single Amino acid Polymorhism detection
proteomics_rnaseq_splice_db_workflow Workflow to create Proteomics Search DB from RNA-seq novel splice detection
rapsodyn Repository with the tools and workflow used for the Rapsodyn project
rapsosnp workflow to detect and select SNP for the rapsodyn project
rapsosnp_v1_5_with_dubious SNP dectection for Brassica Napus with dubious, on Rapsodyn project
riboseqr_wrapper Wrapper for the R package riboSeqR
rnaseq_workflows RNA-seq workflows annotated for use with Refinery Platform
rxlr_venn_workflow Venn diagram comparison of RXLR motif predictions
rxlr_venn_workflow Venn diagram comparison of RXLR motif predictions
secreted_protein_workflow Indentify candidate secreted proteins using SignalP and TMHMM
smart_rda Workflow for RNA-Seq differential expression analysis
sniplay3_complete_workflow SNiPlay3 complete workflow: a package for exploration and large scale analyses of SNP polymorphisms (filtering, density, vcftools, diversity, linkagedisequilibrium, GWAS) (all SNiPlay3 components)
str_fm Pipeline to profile and genotype microsatellites from short read data
venn_list Draw Venn Diagram (PDF) from lists, FASTA files, etc

Data Resources Available in MolBioCloud

Datasets Readily Available Through Shared S3 Bucket

PubChem
MeSH
Entrez Gene
NCBI nr BLAST Database
UniProt
Human Microbiome Project
1000 Genome Project

Available Through On-Demand Request

ENCODE : Encylopedia of DNA Elements
TCGA : The Cancer Genome Atlas Public Data
PDB : RCSB Protein Data Bank
SRA : NCBI Short Read Archive
GEO : NCBI Gene Expression Omnibus