tree-puzzle 5.3.rc16 – Maximum Likelihood Analysis

tree-puzzle 5.3.rc16

:: DESCRIPTION

TREE-PUZZLE is a computer program to reconstruct phylogenetic trees from molecular sequence data by maximum likelihood. It implements a fast tree search algorithm, quartet puzzling, that allows analysis of large data sets and automatically assigns estimations of support to each internal branch. TREEPUZZLE also computes pairwise maximum likelihood distances as well as branch lengths for user specified trees. Branch lengths can be calculated with and without the molecular-clock assumption. In addition, TREE-PUZZLE o ers likelihood mapping, a method to investigate the support of a hypothesized internal branch without computing an overall tree and to visualize the phylogenetic content of a sequence alignment. TREE-PUZZLE also conducts a number of statistical tests on the data set (chi-square test for homogeneity of base composition, likelihood ratio to test the clock hypothesis, one and two-sided Kishino-Hasegawa test, Shimodaira-Hasegawa test, Expected Likelihood Weights). The models of substitution provided by TREE-PUZZLE are GTR, TN, HKY, F84, SH for nucleotides, Dayhoff, JTT, mtREV24, BLOSUM 62, VT, WAG for amino acids, and F81 for two-state data. Rate heterogeneity is modeled by a discrete Gamma distribution and by allowing invariable sites. The corresponding parameters (except for GTR) can be inferred from the data set.

::DEVELOPER

Heiko A. SchmidtArndt von Haeseler

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOSX

:: DOWNLOAD

tree-puzzle

:: MORE INFORMATION

Citation

Schmidt, H.A., K. Strimmer, M. Vingron, and A. von Haeseler (2002)
TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing.
Bioinformatics. 18:502-504.

PSAweb – Analysis of Protein Sequence and Multiple Alignment

PSAweb

:: DESCRIPTION

PSAweb is a web server, developed to analyze the amino acid sequence and multiple sequence alignment of proteins. This is a comprehensive on-line Internet tool that allows the rapid visualization of an analysis, by output in GIF format. It assists the user in analyzing and presenting the primary structure of proteins and mutiple alignment of protein sequences

::DEVELOPER

Dr. G P S Raghava

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Raghava, G. P. S. (2001)
A graphical web server for the analysis of protein sequences and alignment.
Biotech Software and Internet Report 2: 255-8.

MIDAS 1.0 – Analysis and Visualisation of Interallelic Disequilibrium between Multiallelic Markers

MIDAS 1.0

:: DESCRIPTION

MIDAS (Multiallelic Interallelic Disequilibrium Analysis Software) is a linkage disequilibrium analysis program with a comprehensive graphical user interface providing novel views of patterns of linkage disequilibrium between all types of multiallelic and biallelic markers.

::DEVELOPER

The Bristol Genetic Epidemiology Laboratories

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux /Mac OsX / Windows
  • Python

:: DOWNLOAD

 MIDAS

:: MORE INFORMATION

Citation:

Tom R Gaunt, Santiago Rodriguez, Carlos Zapata, Ian NM Day
MIDAS: software for analysis and visualisation of interallelic disequilibrium between multiallelic markers.
BMC Bioinformatics 2006, 7:227 (27 April 2006)

RUM 2.0.5_06 – Comparative Analysis of RNA-Seq Alignment Algorithms and the RNA-Seq Unified Mapper

RUM 2.0.5_06

:: DESCRIPTION

RUM (RNA-Seq Unified Mapper)  is an alignment, junction calling, and feature quantification pipeline specifically designed for Illumina RNA-Seq data.

::DEVELOPER

the Computational Biology and Informatics Laboratory at the University of Pennsylvania

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX
  • Perl

:: DOWNLOAD

 RUM

:: MORE INFORMATION

Citation:

Gregory R. Grant, Michael H. Farkas, Angel Pizarro, Nicholas Lahens, Jonathan Schug, Brian Brunk, Christian J. Stoeckert Jr, John B. Hogenesch and Eric A. Pierce.
Comparative Analysis of RNA-Seq Alignment Algorithms and the RNA-Seq Unified Mapper (RUM)
Bioinformatics. 2011 Sep 15;27(18):2518-28. Epub 2011 Jul 19.

DNA Baser 5.15 – DNA Sequence Assembly & Analysis

DNA Baser 5.15

:: DESCRIPTION

DNA Baser is a tool for DNA sequence assembly, DNA sequence analysis, contig editing, and mutation detection. It also offers a powerful chromatogram viewer/editor.

::DEVELOPER

Heracle BioSoft

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

DNA Baser

:: MORE INFORMATION

CLC Genomics Workbench 12.0.3 – Assembly & Analysis of Sequencing Data

CLC Genomics Workbench 12.0.3

:: DESCRIPTION

CLC Genomics Workbench, for analyzing and visualizing Next Generation Sequencing data, incorporates cutting-edge technology and algorithms, while also supporting and integrating with the rest of your typical NGS workflow.

::DEVELOPER

QIAGEN Bioinformatics

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux /  MacOsX / Window

:: DOWNLOAD

CLC Genomics Workbench Trial

:: MORE INFORMATION

hapLOH 14 – Analysis of loss of Heterozygosity in Tumor Genomes

hapLOH 1.4

:: DESCRIPTION

hapLOH profiles and characterizes tumor genomes using data from SNP microarrays. It is designed to be effective in the presence of high levels of germline contamination.

::DEVELOPER

paul scheet lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX
  • Perl
  • Python

:: DOWNLOAD

  hapLOH

:: MORE INFORMATION

Citation

Vattathil, Selina, and Paul Scheet.
Haplotype-based profiling of subtle allelic imbalance with SNP arrays.
Genome research 23.1 (2013): 152-158.

WinSAAM 3.0 – The Simulation, Analysis and Modeling Software

WinSAAM 3.0

:: DESCRIPTION

WinSAAM is a Windows oriented modeling program enabling the user to explore biological systems using mathematical models. Sophisticated modeling software is required to fit data to such models and to make predictions using these compartmental models. WinSAAM is one such modeling program. The purpose the current report is to describe the features of WinSAAM that make this program suited for modeling all manner of biological systems.

::DEVELOPER

WinSAAM Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 WinSAAM

:: MORE INFORMATION

Citation

Darko Stefanovski, Peter J. Moate and Raymond C. Boston,
WinSAAM: a windows-based compartmental modeling system,
Metabolism, Volume 52, Issue 9, September 2003, Pages 1153-1166.

SNiPlay v3 – SNP and Polymorphism Analysis

SNiPlay v3

:: DESCRIPTION

SNiPlay is a web-based tool for SNP and polymorphism analysis.From sequencing traces, alignment or allelic data given as input, it detects SNP and insertion/deletion events.

::DEVELOPER

SNiPlay team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations.
Dereeper A, Homa F, Andres G, Sempere G, Sarah G, Hueber Y, Dufayard JF, Ruiz M.
Nucleic Acids Res. 2015 Jun 3. pii: gkv351.

BMC Bioinformatics. 2011 May 5;12:134. doi: 10.1186/1471-2105-12-134.
SNiPlay: a web-based tool for detection, management and analysis of SNPs. Application to grapevine diversity projects.
Dereeper A, Nicolas S, Le Cunff L, Bacilieri R, Doligez A, Peros JP, Ruiz M, This P.

Gitools 2.3.1 – Analysis and Visualization of Genomic Data Using Interactive Heat-Maps

Gitools 2.3.1

:: DESCRIPTION

Gitools is a framework for analysis and visualization of genomic data. Data and results are represented as browsable heatmaps. Gitools allows to import data directly from IntOGen and Biomart.

::DEVELOPER

 Gitools Team , Biomedical Genomics Group at the Biomedical Research Park in Barcelona (PRBB)

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/Linux / MacOsX
  • Java

:: DOWNLOAD

 Gitools

:: MORE INFORMATION

Citation

Perez-Llamas, C. & Lopez-Bigas, N.
Gitools: Analysis and Visualisation of Genomic Data Using Interactive Heat-Maps.
PLoS ONE 6, e19541 (2011)