MendelSoft 0.9.8 – Detect Marker Genotyping Incompatibilities

MendelSoft 0.9.8

:: DESCRIPTION

MendelSoft is an open source software which detects marker genotyping incompatibilities (Mendelian errors only) in complex pedigrees using weighted constraint satisfaction techniques. The input of the software is a pedigree data with genotyping data at a single locus. The output of the software is a list of individuals for which the removal of their genotyping data restores consistency. This list is of minimum size when the program ends.

::DEVELOPER

Simon De Givry, BIA, INRA, Toulouse, France @ The Division of Applied Mathematics and Informatics(MIA)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • C++ Compiler

:: DOWNLOAD

 MendelSoft

:: MORE INFORMATION

Citation

M. Sanchez, S. de Givry, and T. Schiex
Mendelian error detection in complex pedigrees using weighted constraint satisfaction techniques
In Constraints journal, special issue on bioinformatics, 13(1), 2008.

REPPER – Detect Regions with Short Gapless REPeats in Protein Sequences

REPPER

:: DESCRIPTION

REPPER (REPeats and their PERiodicities) is an integrated server that detects and analyzes regions with short gapless repeats in protein sequences or alignments. It finds periodicities by Fourier Transform (FTwin) and internal similarity analysis (REPwin). FTwin assigns numerical values to amino acids that reflect certain properties, for instance hydrophobicity, and gives information on corresponding periodicities. REPwin uses self-alignments and displays repeats that reveal significant internal similarities. Both programs use a sliding window to ensure that different periodic regions within the same protein are detected independently. FTwin and REPwin are complemented by secondary structure prediction (PSIPRED) and coiled coil prediction (COILS), making the server a versatile analysis tool for sequences of fibrous proteins.

::DEVELOPER

Söding Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation:

M.Gruber, J. Söding , and A.N.Lupas (2005)
REPPER – repeats and their periodicities in fibrous proteins
Nucl. Acids Res., 33(2), W239-43

cnvHiTSeq 0.1.2 – Detect and Genotype CNVs in WGS data

cnvHiTSeq 0.1.2

:: DESCRIPTION

cnvHiTSeq is a  software for detecting and genotyping CNVs in WGS data

::DEVELOPER

Dr Lachlan J Coin

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Java

:: DOWNLOAD

 cnvHiTSeq

:: MORE INFORMATION

Citation

Genome Biol. 2012 Dec 22;13(12):R120. doi: 10.1186/gb-2012-13-12-r120.
cnvHiTSeq: integrative models for high-resolution copy number variation detection and genotyping using population sequencing data.
Bellos E, Johnson MR, M Coin LJ.

JBD – Detect Binding Sites based on ChIP-chip data and Guides

JBD

:: DESCRIPTION

JBD (Joint Binding Deconvolution) uses additional easily obtainable experimental data about chromatin immunoprecipitation (ChIP) to improve the spatial resolution of the transcription factor binding locations inferred from ChIP followed by DNA microarray hybridization (ChIP-Chip) data.

::DEVELOPER

the Gifford Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/MacOsX
  • Matlab

:: DOWNLOAD

  JBD

:: MORE INFORMATION

Citation

Nat Biotechnol. 2006 Aug;24(8):963-70.
High-resolution computational models of genome binding events.
Qi Y, Rolfe A, MacIsaac KD, Gerber GK, Pokholok D, Zeitlinger J, Danford T, Dowell RD, Fraenkel E, Jaakkola TS, Young RA, Gifford DK.

FiloDetect – Detect & Quantify Filopodia in Single-cell Fluorescence Confocal Microscopy Images

FiloDetect

:: DESCRIPTION

FiloDetect is an image analysis program for detecting and quantifying filopodia in single-cell fluorescence confocal microscopy images.

::DEVELOPER

Perkins Lab at the OHRI

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux / MacOsX /Windows
  •  MatLab

:: DOWNLOAD

 FiloDetect

:: MORE INFORMATION

Citation

S. Nilufar, A. A. Morrow, J. M. Lee, T. J. Perkins
FiloDetect: Automatic Detection of Filopodia from Fluorescence Microscopy Images
BMC Syst Biol. 2013 Jul 23;7:66. doi: 10.1186/1752-0509-7-66.

DeconSeq 0.4.3 – Detect and Remove Contaminations from Metagenomic datasets

DeconSeq 0.4.3

:: DESCRIPTION

DeconSeq is a tool to automatically detect and efficiently remove any type of known sequence contamination from metagenomic datasets. The tool uses a modified version of the BWA-SW aligner and can be applied to longer-read datasets (150+bp read length).

DeconSeq Online Version

::DEVELOPER

the Edwards Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Mac OsX / Linux /
  • Perl

:: DOWNLOAD

 DeconSeq

:: MORE INFORMATION

Citation:

Schmieder R and Edwards R
Fast identification and removal of sequence contamination from genomic and metagenomic datasets.
PLoS ONE 2011, 6:e17288

TagCleaner 0.16 – Detect and Remove Tag Sequences from Metagenomic datasets

TagCleaner 0.16

:: DESCRIPTION

TagCleaner is a tool to automatically detect and efficiently remove tag sequences (e.g. WTA or MID tags) from metagenomic datasets.

TagCleaner Online Version

::DEVELOPER

the Edwards Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac OsX / Linux /
  • Perl

:: DOWNLOAD

 TagCleaner 

:: MORE INFORMATION

Citation:

Schmieder R, Lim YW, Rohwer F, Edwards R
TagCleaner: Identification and removal of tag sequences from genomic and metagenomic datasets.
BMC Bioinformatics 2010, 11:341.

Crann 1.04 – Detect Adaptive Evolution in Protein-coding DNA Sequences

Crann 1.04

:: DESCRIPTION

Crann (pronounced ‘crown’) is the Irish word for ‘tree’.Crann has been developed in order to provide fast heuristic methods of detecting adaptive evolution in protein-coding genes. It is important that the user understands the advantages and limitations of these methods. It is also important for the user to know that the software is designed to perform a number of different tasks, however the interpretation of the results is left entirely to the user.

::DEVELOPER

McInerney lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOS

:: DOWNLOAD

Crann

:: MORE INFORMATION

Citation:

Creevey, C. and J. O. McInerney (2003).
CRANN: Detecting adaptive evolution in protein-coding DNA sequences
Bioinformatics (2003) 19: 1726.

GISTIC 2.0.22 – Detect Regions of Significant Copy-number Gains and Losses

GISTIC 2.0.22

:: DESCRIPTION

GISTIC  (Genomic Identification of Significant Targets in Cancer) facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers

::DEVELOPER

The Cancer Genome Analysis (CGA) group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 GISTIC

:: MORE INFORMATION

Citation

Genome Biol. 2011;12(4):R41. Epub 2011 Apr 28.
GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers.
Mermel CH, Schumacher SE, Hill B, Meyerson ML, Beroukhim R, Getz G.

RepWords 1.1 – Detect Tandem Repeats in FASTA Sequences

RepWords 1.1

:: DESCRIPTION

RepWords detects tandem repeats in FASTA sequences.

::DEVELOPER

Statistical Computational Biology Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / WIndows / MacOsX
  • C++ Compiler

:: DOWNLOAD

 RepWords

:: MORE INFORMATION

Citation

Int J Bioinform Res Appl. 2014;10(4):384-408. doi: 10.1504/IJBRA.2014.062991.
Searching for repeats, as an example of using the generalised Ruzzo-Tompa algorithm to find optimal subsequences with gaps.
Spouge JL, Mariño-Ramírez L, Sheetlin SL.