Tag: Analyse

Endog 4.8 – Analyse Pedigree Information

Endog 4.8

:: DESCRIPTION

ENDOG‘s Primary functions are the computation of the individual inbreeding (F) (Wright, 1931) and the average relatedness (AR) (Gutiérrez et al., 2003; Goyache et al., 2003) coefficients. Additionally, users can compute with ENDOG useful parameters in population genetics such as that described for Biochard et al. (1997) for the number of ancestors explaining genetic variability or those proposed by Robertson (1953) and Vassallo et al. (1996) for the genetic importance of the herds. ENDOG also can compute F statistics (Wright, 1978) from genealogical information following Caballero and Toro (2000; 2002). Moreover, the present version of ENDOG calculates effective population size following different methodologies including regression approaches and particularly the recently proposed realized effective population size from individual increase in inbreeding (Gutiérrez et al., 2008), modified to account for avoidance of self-fertilization (Gutiérrez et al., 2009).

::DEVELOPER

Juan Pablo Gutiérrez García

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 Endog

:: MORE INFORMATION

Citation

A note on ENDOG: a computer program for analysing pedigree information.
Gutiérrez JP, Goyache F.
J Anim Breed Genet. 2005 Jun;122(3):172-6.

Coancestry 1.0.1.2 – Simulate, Estimate and Analyse Relatedness and Inbreeding Coefficients

Coancestry 1.0.1.2

:: DESCRIPTION

COANCESTRY is a computer program that implements 7 methods to estimate the pairwise relatedness between individuals and 4 methods to estimate individual inbreeding coefficients, using individual genotypes at a set of marker loci.

:: DEVELOPER

Dr Jinliang Wang

:: SCREENSHOTS

Coancestry

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 Coancestry

:: MORE INFORMATION

Citation

COANCESTRY: a program for simulating, estimating and analysing relatedness and inbreeding coefficients.
Wang J.
Mol Ecol Resour. 2011 Jan;11(1):141-5. doi: 10.1111/j.1755-0998.2010.02885.x.

NNPERM 1.3 – Analyse Case-control Multi-locus Genotype Data

NNPERM 1.3

:: DESCRIPTION

NNPERM is a neural network program for analysing case-control multi-locus genotype data using a permutation test.

::DEVELOPER

Bernard North

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

NNPERM

:: MORE INFORMATION

Citation:

B.V. North, D. Curtis, P.G.Cassell, G.A.Hitman and P. C. Sham
Assessing optimal neural network architecture for identifying disease-associated multi-marker genotypes using a permutation test, and application to calpain 10 polymorphisms associated with diabetes.
Annals of Human Genetics 67: 348-356

Stacks 2.59 – Analyse RAD Sequencing data

Stacks 2.59

:: DESCRIPTION

Stacks is a software pipeline for building loci out of a set of short-read sequenced samples. Stacks was developed for the purpose of building genetic maps from RAD-Tag Illumina sequence data, but can also be readily applied to population studies, and phylogeography.

DEVELOPER

Cresko labs

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 Stacks

:: MORE INFORMATION

Citation:

J. Catchen, A. Amores, P. Hohenlohe, W. Cresko, and J. Postlethwait.
Stacks: building and genotyping loci de novo from short-read sequences.
G3: Genes, Genomes, Genetics, 1:171-182, 2011

BiNoM 2.5 – Cytoscape plug-in for Manipulating and Analysing biological networks

BiNoM 2.5

:: DESCRIPTION

BiNoM (Biological Network Manager )is a Cytoscape plugin, developed to facilitate the manipulation of biological networks represented in standard systems biology formats (SBML, SBGN, BioPAX) and to carry out studies on the network structure. BiNoM provides the user with a complete interface for the analysis of biological networks in Cytoscape environment.

::DEVELOPER

Computational Systems Biology of Cancer group in Bioinformatics Laboratory of Institut Curie (Paris).

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 BiNoM

:: MORE INFORMATION

Citation:

BiNoM 2.0, a Cytoscape plugin for accessing and analyzing pathways using standard systems biology formats.
Bonnet E, Calzone L, Rovera D, Stoll G, Barillot E, Zinovyev A.
BMC Syst Biol. 2013 Mar 1;7:18. doi: 10.1186/1752-0509-7-18.

Zinovyev A., Viara E., Calzone L., Barillot E.
BiNoM: a Cytoscape plugin for manipulating and analyzing biological networks. 2008.
Bioinformatics 24(6):876-877

SLiMSuite v1.9.1 – Bioinformatics Tools to Analyse Protein Features

SLiMSuite v1.9.1

:: DESCRIPTION

The SLiMSuite collection contains a number of open-source bioinformatics tools to analyse these important protein features. The main programs in SLiMSuite are: SLiMFinder, SLiMSearch, QSLiMFinder, SLiMDisc, SLiMPred, SLiMPrints, CompariMotif, SLiMMaker, PRESTO and GOPHER.

::DEVELOPER

EdwardsLab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / Mac OsX
  • Python

:: DOWNLOAD

 SLiMSuite

:: MORE INFORMATION

Citation:

Bioinformatics. 2015 Mar 19. pii: btv155.
QSLiMFinder: improved short linear motif prediction using specific query protein data.
Palopoli N, Lythgow KT, Edwards RJ

Davey NE, Cowan JL, Shields DC, Gibson TJ, Coldwell MJ, Edwards RJ
SLiMPrints: conservation-based discovery of functional motif fingerprints in intrinsically disordered protein regions.
Nucl. Acids Res. (2012)doi: 10.1093/nar/gks854

Davey NE, Haslam NJ, Shields DC & Edwards RJ (2011):
SLiMSearch 2.0: biological context for short linear motifs in proteins.
Nucleic Acids Research 39: W56-W60

Davey NE, Haslam NJ, Shields DC & Edwards RJ (2010):
SLiMFinder: a web server to find novel, significantly over-represented, short protein motifs.
Nucleic Acids Research 38: W534-W539.

Davey NE*, Edwards RJ* & Shields DC (2007):
The SLiMDisc server: short, linear motif discovery in proteins.
Nucleic Acids Res. 35(Web Server issue):W455-9.

Edwards RJ, Davey NE & Shields DC (2008):
CompariMotif: Quick and easy comparisons of sequence motifs.
Bioinformatics 24(10):1307-9

Quarc 1.0 – Analyse a set of Short Read data

Quarc 1.0

:: DESCRIPTION

Quarc (Quality Analysis and Read Control) contains a couple of useful programs to analyse a set of short read data

::DEVELOPER

Jan Schroeder <schroder@csse.unimelb.edu.au>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Quarc

:: MORE INFORMATION

Citation

Reference-free validation of short read data.
Schröder J, Bailey J, Conway T, Zobel J.
PLoS One. 2010 Sep 22;5(9):e12681. doi: 10.1371/journal.pone.0012681.

AgileKnownSNPFilter 20120105 – Analyses Sequence Variants

AgileKnownSNPFilter 20120105

:: DESCRIPTION

AgileKnownSNPFilter analyses sequence variants exported by AgileAnnotator and identifies those that have previously been found by the 1000 Genomes Project.

::DEVELOPER

Ian’s DNA@Leeds

:: SCREENSHOTS

AgileKnownSNPFilter

:: REQUIREMENTS

  • Windows
  • Microsoft .NET framework version 2.0 

:: DOWNLOAD

 AgileKnownSNPFilter

:: MORE INFORMATION

ChIPMonk 1.2.3 – Visualise and Analyse ChIP-on-chip Array data

ChIPMonk 1.2.3

:: DESCRIPTION

ChIPMonk is a program designed to help in the visualisation and analysis of ChIP-on-chip array data. It provides a comprehensive set of tools to import, normalise, analyse and visualise your data.

:: DEVELOPER

Babraham Bioinformatics

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Mac OsX/Windows
  • Java 

:: DOWNLOAD

 ChIPMonk

:: MORE INFORMATION

PoPoolation 1.2.2 / PoPoolation2 1.201 / PoPoolation TE 1.02 – Analyse Pooled Next Generation Sequencing data

popoolation 1.2.2 / PoPoolation2 1.201 / PoPoolation TE 1.02

:: DESCRIPTION

PoPoolation is a collection of tools to facilitate population genetic studies of next generation sequencing data from pooled individuals

PoPoolation2 allows to compare allele frequencies for SNPs between two or more populations and to identify significant differences.

PoPoolation TE is a quick and simple pipeline for the analysis of transposable element insertions in (natural) populations using next generation sequencing.

DEVELOPER

Institute of Population Genetics, University of Veterinary Medicine Vienna

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 popoolation , PoPoolation2

:: MORE INFORMATION

Citation:

PoPoolation: a toolbox for population genetic analysis of next generation sequencing data from pooled individuals.
Kofler R, Orozco-terWengel P, De Maio N, Pandey RV, Nolte V, Futschik A, Kosiol C, Schlštterer C.
PLoS One. 2011 Jan 6;6(1):e15925.

Kofler,R.,Vinay Pandey, R. & Schloetterer, C
PoPoolation2: Identifying differentiation between populations using sequencing of pooled DNA samples (Pool-Seq);
Bioinformatics; Vol. 27 no. 24 2011, pages 3435–3436; doi:10.1093/bioinformatics/btr589

Robert Kofler, Andrea Betancourt and Christian Schloetterer (2012):
Sequencing of Pooled DNA Samples (Pool-Seq) Uncovers Complex Dynamics of Transposable Element Insertions in Drosophila melanogaster;
PLoS Genet 8(1): e1002487. doi:10.1371/journal.pgen.1002487