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

PhyloGenie – Automating Phylome Analysis

PhyloGenie

:: DESCRIPTION

PhyloGenie is a PERL script combining the various steps necessary to producing a phylome. BLAST or PSIBLAST searches are performed for all FASTA format sequences in an input file, the HSP’s corresponding to user defined selection criteria (E-value, coverage, score per column, identity) are extracted and used as a basis for multiple sequence alignment. Phylogenies can then be infered using the supplied standard NJ method or any other program accepting aligned FASTA sequences as input and generating Newick format trees. As analysis of phylogenies is far more complex than analysis of BLAST results we also provide a tool to filter a set of phylogenetic trees for those corresponding to user defined topological selection criteria.

::DEVELOPER

PhyloGenie team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 PhyloGenie

:: MORE INFORMATION

Citation

Frickey T., Lupas A.N., (2004)
PhyloGenie: automated phylome generation and analysis.
Nucleic Acids Res., 32(17): 5231-8.

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.

SLiMSuite 20150107 – Bioinformatics Tools to Analyse Protein Features

SLiMSuite 20150107

:: 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

Dr Richard J. Edwards

:: 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

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

Stacks 1.29 – Analyse RAD Sequencing data

Stacks 1.29

:: 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

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

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.

SPANS 1.0 – Statistical Procedure for the Analyses of peptide abundance Normalization Strategies

SPANS 1.0

:: DESCRIPTION

SPANS is an approach to evaluate normalization strategies, which includes the peptide selection component associated with the derivation of normalization values. The approach evaluates the effect of normalization on the between-group variance structure in order to identify the most appropriate normalization methods that improve the structure of the data without introducing bias into the normalized peak intensities.

::DEVELOPER

Computational Biology & Bioinformatics ,Pacific Northwest National Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows
  • Java
  • matlab

:: DOWNLOAD

 SPANS

:: MORE INFORMATION

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

Leeds Institute of Molecular Medicine

:: SCREENSHOTS

AgileKnownSNPFilter

:: REQUIREMENTS

  • Windows
  • Microsoft .NET framework version 2.0 

:: DOWNLOAD

 AgileKnownSNPFilter

:: MORE INFORMATION