HAC 1.2.1 – Hierarchical Agglomerative Clustering for a large-scale Network data

HAC 1.2.1

:: DESCRIPTION

HAC is developed for fast clustering of heterogeneous interaction networks.

::DEVELOPER

Joel Bader lab

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux

:: DOWNLOAD

 HAC

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2011 Feb 15;12 Suppl 1:S44. doi: 10.1186/1471-2105-12-S1-S44.
Resolving the structure of interactomes with hierarchical agglomerative clustering.
Park Y, Bader JS.

MegaDot 0.9 – Large Scale Dot Plotter

MegaDot 0.9

:: DESCRIPTION

MegaDot is a large scale dot plotter which is capable of producing dot density plots of tens of megabases of DNA sequence on a modest sized desktop machine, and of entire mammalian chromosomes on server scale computers.

::DEVELOPER

Human Genome Sequencing Center, Baylor College of Medicine

:: SCREENSHOTS

megadot

:: REQUIREMENTS

  • Windows  / Linux / MacOsX
  • Java

:: DOWNLOAD

 MegaDot

:: MORE INFORMATION

Giggle v0.6.3 – Search Engine for large-scale integrated Genome Analysis

Giggle v0.6.3

:: DESCRIPTION

Giggle is a genomics search engine for genomic features and intervals. That is, scalable, multi-file index for fast queries of genomic intervals.

::DEVELOPER

The Quinlan Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

Giggle

:: MORE INFORMATION

Citation:

Nat Methods. 2018 Feb;15(2):123-126. doi: 10.1038/nmeth.4556. Epub 2018 Jan 8.
GIGGLE: a search engine for large-scale integrated genome analysis.
Layer RM, Pedersen BS, DiSera T, Marth GT, Gertz J, Quinlan AR

SNAVI 20081120 – Analysis and Visualization of Large-Scale Cell Signaling Networks

SNAVI 20081120

:: DESCRIPTION

SNAVI (Signaling Networks Analysis and Visualization) is a Windows-based desktop application that implements standard network analysis methods to compute the clustering, connectivity distribution, and detection of network motifs, as well as provides means to visualize networks and network motifs. SNAVI is capable of generating linked web pages from network datasets loaded in text format. SNAVI can also create networks from lists of gene or protein names. SNAVI is a useful tool for analyzing, visualizing and sharing cell signaling data. SNAVI is open source free software.

::DEVELOPER

Ma’ayan Laboratory

:: SCREENSHOTS

SNAVI

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 SNAVI

:: MORE INFORMATION

Citation

BMC Syst Biol. 2009 Jan 20;3:10. doi: 10.1186/1752-0509-3-10.
SNAVI: Desktop application for analysis and visualization of large-scale signaling networks.
Ma’ayan A, Jenkins SL, Webb RL, Berger SI, Purushothaman SP, Abul-Husn NS, Posner JM, Flores T, Iyengar R.

MUMmer 4.0.0Beta2 / pymummer 0.11.0 – Alignment of Large-scale DNA & Protein Sequences

MUMmer 4.0.0Beta2/ pymummer 0.11.0

:: DESCRIPTION

MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form.MUMmer can also align incomplete genomes; it can easily handle the 100s or 1000s of contigs from a shotgun sequencing project, and will align them to another set of contigs or a genome using the NUCmer program included with the system. If the species are too divergent for a DNA sequence alignment to detect similarity, then the PROmer program can generate alignments based upon the six-frame translations of both input sequences.

pymummer is Python3 module for running MUMmer and reading the output

::DEVELOPER

MUMmer team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • GCC / Python

:: DOWNLOAD

MUMmer, pymummer

:: MORE INFORMATION

MUMmer is now an open source project.

Citation:

MUMmer4: A fast and versatile genome alignment system
G. Marçais , A.L. Delcher, A.M. Phillippy, R. Coston, S.L. Salzberg, A. Zimin,
PLoS computational biology (2018), 14(1): e1005944.

MR-MSPOLYGRAPH / MSPolygraph 1.61 – MapReduce Implementation of a Hybrid Spectral Library-Database Search Method for Large-scale Peptide Identification

MR-MSPOLYGRAPH / MSPolygraph 1.61

:: DESCRIPTION

MR-MSPOLYGRAPH is a MapReduce based implementation for parallelizing peptide identification from mass spectrometry data

MSPolygraph is an open source hybrid database and spectral library MS/MS search engine that runs in either serial or parallel modes. MSPolygraph examines the ions in MS/MS spectra to identify likely matching candidate peptides from a reference database of protein sequences (.Fasta file). MSPolygraph also supports searching a spectral library (collection of annotated MS/MS spectra).

::DEVELOPER

Ananth Kalyanaraman

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

 MR-MSPOLYGRAPH / MSPolygraph

:: MORE INFORMATION

Citation

A. Kalyanaraman, W.R. Cannon, B. Latt, D.J. Baxter (2011).
MapReduce implementation of a hybrid spectral library-database search method for large-scale peptide identification.
Bioinformatics (2011) 27 (21): 3072-3073. doi: 10.1093/bioinformatics/btr523.

Cannon W.R., K.H. Jarman, B.M. Webb-Robertson, D.J. Baxter, C.S. Oehmen, K.D. Jarman, A. Heredia-Langner, G.A. Anderson, and K.J. Auberry. 2005.
Comparison of probability and likelihood models for peptide identification from tandem mass spectrometry data”,
J. Proteome Research, 4(5): 1687-169

CloudNMF – MapReduce implementation of NMF for large scale Biological datasets

CloudNMF

:: DESCRIPTION

CloudNMF is a distributed open-source implementation of NMF (nonnegative Matrix Factorization) on a MapReduce framework.

::DEVELOPER

CloudNMF team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 CloudNMF

:: MORE INFORMATION

Citation:

Genomics Proteomics Bioinformatics. 2014 Feb;12(1):48-51. doi: 10.1016/j.gpb.2013.06.001. Epub 2013 Aug 8.
CloudNMF: a MapReduce implementation of nonnegative matrix factorization for large-scale biological datasets.
Liao R, Zhang Y, Guan J, Zhou S

pGraph / psgraph 3.0 – Parallel Construction of large-scale Protein Sequence Homology Graphs

pGraph 3.0

:: DESCRIPTION

 pGraph /psgraph (parallel sequence graph construction)  is a novel hybrid between the hierarchical multiple-master/worker model and producer-consumer model, and is designed to break the irregularities imposed by alignment computation and work generation.

::DEVELOPER

Ananth Kalyanaraman

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

 pGraph / psgraph

:: MORE INFORMATION

Citation

C. Wu, A. Kalyanaraman, W. Cannon.
pGraph: Efficient parallel construction of large-scale protein sequence homology graphs.
IEEE Transactions on Parallel and Distributed Systems Volume: 23 , Issue: 10 Page(s): 1923 – 1933

DupTree – Large Scale Gene Tree Parsimony Analysis

DupTree

:: DESCRIPTION

DupTree is a program for large-scale phylogenetic analyses using gene tree parsimony.The program implements a novel algorithm that significantly improves upon the run time of standard search heuristics for gene tree parsimony, and enables the first truly genome-scale phylogenetic analyses.

::DEVELOPER

Computational Biology Laboratory, Department of Computer Science,Iowa State University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX

:: DOWNLOAD

  DupTree

:: MORE INFORMATION

Citation

DupTree: A program for large-scale phylogenetic analyses using gene tree parsimony
Andre Wehe, Mukul S. Bansal, J. G. Burleigh, Oliver Eulenstein.
Bioinformatics, 24(13): 1540-1541, 2008.

phenomeImpute 1.0 – R package to Impute Missing values in large-scale High-dimensional Phenome data

phenomeImpute 1.0

:: DESCRIPTION

phenomeImpute is an R package to impute missing values in large-scale high-dimensional phenome data. It includes several variations of KNN, random forest and MICE methods.

::DEVELOPER

George C. Tseng 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 phenomeImpute

:: MORE INFORMATION

Citation

Serena G. Liao&, Yan Lin&, Dongwan Kang, Naftali Kaminski, Frank C. Sciurba, George C. Tseng. (2014)
Missing value imputation in high-dimensional phenomic data: Imputable or not? And how?.
In preparation.