rate4site 2.01 – Detect Conserved Amino-acid Site

rate4site 2.01

:: DESCRIPTION

rate4site is a program for detecting conserved amino-acid sites by computing the relative evolutionary rate for each site in a multiple sequence alignment.

::DEVELOPER

Mayrose Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux

:: DOWNLOAD

  rate4site

:: MORE INFORMATION

Citation

Mayrose, I., Graur, D., Ben-Tal, N., and Pupko, T. 2004.
Comparison of site-specific rate-inference methods: Bayesian methods are superior.
Mol Biol Evol 21: 1781-1791.

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.

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.

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

GeneSyn 1.1 – Detect Conserved Gene Order across Genomes

GeneSyn 1.1

:: DESCRIPTION

GeneSyn is a software for the detection of highly conserved gene arrangements through the analysis of multiple gene orders in different genomes.

::DEVELOPER

Giulio Pavesi

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 GeneSyn

:: MORE INFORMATION

Citation:

GeneSyn: a tool for detecting conserved gene order across genomes.
Pavesi G, Mauri G, Iannelli F, Gissi C, Pesole G.
Bioinformatics. 2004 Jun 12;20(9):1472-4. Epub 2004 Feb 19.

i-ADHoRe 3.0 – Detect Degenerated Genomic Homology

i-ADHoRe 3.0

:: DESCRIPTION

i-ADHoRe is a highly sensitive software tool to detect degenerated homology relations within and between different genomes.

::DEVELOPER

Van de Peer Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

  i-ADHoRe

:: MORE INFORMATION

Citation

i-ADHoRe 3.0–fast and sensitive detection of genomic homology in extremely large data sets.
Proost S, Fostier J, De Witte D, Dhoedt B, Demeester P, Van de Peer Y, Vandepoele K.
Nucleic Acids Res. 2012 Jan;40(2):e11. doi: 10.1093/nar/gkr955.

Simillion, C., Janssens, K., Sterck, L., Van de Peer, Y. (2008)
i-ADHoRe 2.0: An improved tool to detect degenerated genomic homology using genomic profiles.
Bioinformatics 24, 127-8.

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.