OrthoMCL 2.0.9 – Genome-scale Algorithm for Grouping Orthologous Protein Sequences

OrthoMCL 2.0.9

:: DESCRIPTION

OrthoMCL is a genome-scale algorithm for grouping orthologous protein sequences. It provides not only groups shared by two or more species/genomes, but also groups representing species-specific gene expansion families. So it serves as an important utility for automated eukaryotic genome annotation. OrthoMCL starts with reciprocal best hits within each genome as potential in-paralog/recent paralog pairs and reciprocal best hits across any two genomes as potential ortholog pairs. Related proteins are interlinked in a similarity graph.

::DEVELOPER

OrthoMCL team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
perl
BLAST
MySql

:: DOWNLOAD

OrthoMCL

:: MORE INFORMATION

Citation

Li Li, Christian J. Stoeckert, Jr., and David S. Roos
OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes
Genome Res. 2003 13: 2178-2189

Illuminus – Genotype Calling algorithm

Illuminus

:: DESCRIPTION

Illuminus is a program that calls genotype from the Illumina BeadArray platform which does not rely on having prior training data or require computationally intensive procedures. The algorithm can assign genotypes to hybridization data from thousands of individuals simultaneously and pools information across multiple individuals to improve the calling. The method can accommodate variations in hybridization intensities which result in dramatic shifts of the position of the genotype clouds by identifying the optimal coordinates to initialize the algorithm.

::DEVELOPER

Saw Swee Hock School of Public Health

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/ Windows/ MacOsX
C++ Compiler

:: DOWNLOAD

Illuminus

:: MORE INFORMATION

Citation

Teo YY, Inouye M, Small KS, Gwilliam R, Deloukas P, Kwiatkowski DP and Clark TG. (2007)
A genotype calling algorithm for the Illumina BeadArray platform.
Bioinformatics (Oxford, England), 23(20), 2741-2746

optiCall 0.8.1 – Robust Genotype-calling Algorithm

optiCall 0.8.1

:: DESCRIPTION

optiCall is a robust genotype-calling algorithm for calling rare, low-frequency and common variants from SNP microarray intensity data.

::DEVELOPER

Tejas Shah & Carl Anderson (opticall@sanger.ac.uk.)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / MacOsX

:: DOWNLOAD

optiCall

:: MORE INFORMATION

Citation

T. S. Shah, J. Z. Liu, J. A. B. Floyd, J. A. Morris, N. Wirth, J. C. Barrett and C. A. Anderson
optiCall: a robust genotype-calling algorithm for rare, low-frequency and common variants
Bioinformatics (2012) 28 (12): 1598-1603.

Telescoper 0.2 – De novo Assembly Algorithm

Telescoper 0.2

:: DESCRIPTION

Telescoper is a local assembly algorithm designed for short-reads from NGS platforms such as Illumina. The reads must come from two libraries: one short insert, and one long insert.

::DEVELOPER

Yun S. Song

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Python

:: DOWNLOAD

Telescoper

:: MORE INFORMATION

Citation

Bresler, M., Sheehan, S., Chan, A.H., and Song, Y.S.
Telescoper: De novo Assembly of Highly Repetitive Regions.
Bioinformatics, 28 (2012) i311-i317.

DSA 1.0 – Digital Sorting Algorithm for Heterogeneous Samples

DSA 1.0

:: DESCRIPTION

DSA is a software for extracting cell-type specific gene expression profiles from mixed tissue samples that is unbiased and does not require prior knowledge of cell type frequencies.

:: DEVELOPER

Liu Lab, Baylor College of Medicine

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / windows/ MacOsX
R

:: DOWNLOAD

DSA

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2013 Mar 7;14:89. doi: 10.1186/1471-2105-14-89.
Digital sorting of complex tissues for cell type-specific gene expression profiles.
Zhong Y1, Wan YW, Pang K, Chow LM, Liu Z.

TPM – Temporal Pattern Mining Algorithm

TPM

:: DESCRIPTION

TPM algorithm clusters any time-series data set, specifically iTRAQ LC-MS/MS data sets. The data points that have a similar behavior over the time course are clustered together.

::DEVELOPER

Epithelial Systems Biology Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

Fahad Saeed, Trairak Pisitkun, Mark Knepper and Jason D Hoffert,
“Mining Temporal Patterns from iTRAQ Mass Spectrometry (LC-MS/MS) Data“,
The Proceedings of the ISCA 3rd International Conference on Bioinformatics and Computational Biology (BiCoB), Vol 1. pp 152-159 New Orleans, Louisiana, USA, March 23-25, 2011 (ISBN: 978-1-880843-81-9)

reHCstar 2.1.5 – Algorithm for Haplotype Inference problem on Pedigree data with Recombinations, Errors and Mutations

reHCstar 2.1.5

:: DESCRIPTION

reHCstar is a SAT-based program to compute a haplotype configuration on pedigrees with recombinations, genotyping errors, and missing genotypes.

::DEVELOPER

AlgoLab

:: SCREENSHOTS

N/A

::REQUIREMENTS

Linux
CMake
GNU make
Boost FileSystem, System, DateTime, ProgramOptions, IOStreams, and other include-only libraries
Apache Log4cxx

:: DOWNLOAD

reHCstar

:: MORE INFORMATION

Citation

Yuri Pirola, Gianluca Della Vedova, Stefano Biffani, Alessandra Stella, and Paola Bonizzoni.
A fast and practical approach to genotype phasing and imputation on a pedigree with erroneous and incomplete information.
IEEE/ACM Transactions on Computational Biology and Bioinformatics (2012).

ADDA version 4 – Automatic Domain Decomposition Algorithm

ADDA version 4

:: DESCRIPTION

ADDA is an automatic algorithm for domain decomposition and clustering of all protein domain families. the authors use alignments derived from an all-on-all sequence comparison to define domains within protein sequences based on a global maximum likelihood model.

::DEVELOPER

The Institute of Biotechnology (BI) at the University of Helsinki

:: SCREENSHOTS

N/A

::REQUIREMENTS

Linux
MySQL

:: DOWNLOAD

ADDA

:: MORE INFORMATION

Citation

Heger A, Holm L (2003)
Exhaustive enumeration of protein families.
J Mol Biol 328(3):749-67.

MeDiChI 0.4.1 – Model-Based ChIP-chip Deconvolution Algorithm

MeDiChI 0.4.1

:: DESCRIPTION

MeDiChI is method for the automated, model-based deconvolution of protein-DNA binding (Chromatin immunoprecipitation followed by hybridization to a genomic tiling microarray — ChIP-chip) data that discovers DNA binding sites at high resolution (higher resolution than that of the tiling array itself).

::DEVELOPER

Baliga Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/Linux/MacOsX
R package

:: DOWNLOAD

MeDiChI

:: MORE INFORMATION

Citation

Bioinformatics. 2008 Feb 1;24(3):396-403. Epub 2007 Dec 1.
Model-based deconvolution of genome-wide DNA binding.
Reiss DJ, Facciotti MT, Baliga NS.

ProPhylo 1.02 – Phylogenetic Profile comparison program using Partial Phylogenetic Profile algorithm

ProPhylo 1.02

:: DESCRIPTION

ProPhylo is a high-performance parallel software to run phylogenetic profile searches at genome-scale.

::DEVELOPER

Malay K Basu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Perl

:: DOWNLOAD

ProPhylo

:: MORE INFORMATION

Citation

Basu, M. K., Selengut, J. D., Haft, D. H.
ProPhylo: partial phylogenetic profiling to guide protein family construction and assignment of biological process
BMC Bioinformatics. 2011 Dec 01; 12: 434.