simLoci 1.0 – Simulate Sequence data on an input Topology

 DNA / Genome Analysis 9 views Comments Off on simLoci 1.0 – Simulate Sequence data on an input Topology
Jul 162015
 

simLoci 1.0

:: DESCRIPTION

The script simLoci.py can be used to simulate sequence data on an input topology under a coalescent model with arguments to allow migration between lineages and to modify population parameters.

::DEVELOPER

Deren Eaton

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX / Windows
  • Python

:: DOWNLOAD

 simLoci

:: MORE INFORMATION

PyRAD 3.0.5 – Assembly of de novo RADseq loci for Phylogenetic Analyses

 Phylogenetic Analysis 44 views Comments Off on PyRAD 3.0.5 – Assembly of de novo RADseq loci for Phylogenetic Analyses
Jul 162015
 
PyRAD 3.0.5 - Assembly of de novo RADseq loci for Phylogenetic Analyses

PyRAD 3.0.5 :: DESCRIPTION PyRAD is a pipeline to assemble de novo RADseq loci with the aim of optimizing coverage across phylogenetic datasets. ::DEVELOPER Deren Eaton :: SCREENSHOTS N/A :: REQUIREMENTS Linux/ MacOsX / Windows Python :: DOWNLOAD  PyRAD :: MORE INFORMATION Citation Bioinformatics. 2014 Mar 20. PyRAD: assembly of de novo RADseq loci for phylogenetic […]

simRRLs 1.5 – Simulate fastQ formatted RAD, ddRAD or GBS data on a fixed Species Tree

 Phylogenetic Analysis 15 views Comments Off on simRRLs 1.5 – Simulate fastQ formatted RAD, ddRAD or GBS data on a fixed Species Tree
Jul 162015
 
simRRLs 1.5 - Simulate fastQ formatted RAD, ddRAD or GBS data on a fixed Species Tree

simRRLs 1.5 :: DESCRIPTION The script simRRLs.py can be used to simulate RADseq-like sequences on a fixed species tree under a coalescent model. See Example usage page for advanced options, including simulating missing data, indels and different levels of divergence between taxa. ::DEVELOPER Deren Eaton :: SCREENSHOTS N/A :: REQUIREMENTS Linux/ MacOsX / Windows Python […]

PhyML 20141029 – Phylogeny software based on the Maximum Likelihood

 Phylogenetic Analysis 987 views Comments Off on PhyML 20141029 – Phylogeny software based on the Maximum Likelihood
Jul 162015
 
PhyML 20141029 - Phylogeny software based on the Maximum Likelihood

PhyML 20141029 :: DESCRIPTION PhyML (Phylogenetic estimation using Maximum Likelihood) is a phylogeny software based on the maximum-likelihood principle. Early PhyML versions used a fast algorithm to perform Nearest Neighbor Interchanges (NNIs), in order to improve a reasonable starting tree topology. PhyML Online Version ::DEVELOPER Stéphane Guindon , Olivier Gascuel :: SCREENSHOTS N/A :: REQUIREMENTS Windows / MacOsX […]

LayerCake – Visual Comparison of Viral Deep Sequencing data

 DNA / Genome Analysis 3 views Comments Off on LayerCake – Visual Comparison of Viral Deep Sequencing data
Jul 142015
 
LayerCake - Visual Comparison of Viral Deep Sequencing data

LayerCake :: DESCRIPTION LayerCake is a tool created for visualizing viral variation from next generation sequencing data ::DEVELOPER collaboration between labs associated with UW Computer Sciences andUW Pathology & Laboratory Medicine Departments. :: SCREENSHOTS :: REQUIREMENTS Windows / MacOsX Java :: DOWNLOAD  LayerCake :: MORE INFORMATION Citation LayerCake: a tool for the visual comparison of viral […]

DINGO 1.0 – Differential Network Analysis in Genomics

 System Biology & Modeling 5 views Comments Off on DINGO 1.0 – Differential Network Analysis in Genomics
Jul 142015
 
DINGO 1.0 - Differential Network Analysis in Genomics

DINGO 1.0 :: DESCRIPTION DINGO is a pathway-based differential network analysis in genomics model for estimating group-specific networks as well as making inference on the differential networks. ::DEVELOPER Min Jin Ha <mjha@mdanderson.org>, Veerabhadran Baladandayuthapani , Kim-Anh Do :: SCREENSHOTS N/A :: REQUIREMENTS Windows / Linux / MacOsX R :: DOWNLOAD  DINGO :: MORE INFORMATION Citation: DINGO: Differential Network […]

TSSi 1.14.0 – Transcription Start Site Identification

 RNA Analysis 4 views Comments Off on TSSi 1.14.0 – Transcription Start Site Identification
Jul 142015
 
TSSi 1.14.0 - Transcription Start Site Identification

TSSi 1.14.0 :: DESCRIPTION The TSSi package identifies and normalizes transcription start sites in high-throughput sequencing data. ::DEVELOPER Julian Gehring, Clemens Kreutz :: SCREENSHOTS N/A :: REQUIREMENTS Windows / Linux / MacOsX R :: DOWNLOAD  TSSi :: MORE INFORMATION Citation: TSSi–an R package for transcription start site identification from 5′ mRNA tag data. Kreutz C, Gehring […]

Data2Dynamics – Modeling Environment Tailored to Parameter Estimation in Dynamical System

 System Biology & Modeling 4 views Comments Off on Data2Dynamics – Modeling Environment Tailored to Parameter Estimation in Dynamical System
Jul 142015
 
Data2Dynamics - Modeling Environment Tailored to Parameter Estimation in Dynamical System

Data2Dynamics :: DESCRIPTION The Data2Dynamics software package is a collection of numerical methods for quantitative dynamic modeling and a comprehensive model and data description language. The software facilitates the construction of dynamical models for biochemical reaction networks, but is not limited to this. ::DEVELOPER D2D development team :: SCREENSHOTS N/A :: REQUIREMENTS Windows / Linux […]

APE 3.3 – Analysis of Phylogenetics and Evolution

 Phylogenetic Analysis 529 views Comments Off on APE 3.3 – Analysis of Phylogenetics and Evolution
Jul 142015
 
APE 3.3 - Analysis of Phylogenetics and Evolution

APE 3.3 :: DESCRIPTION APE (Analysis of Phylogenetics and Evolution) is a package for the analysis of phylogenetics and evolution.APE provides functions for reading, writing, plotting, and manipulating phylogenetic trees, analyses of comparative data in a phylogenetic framework, analyses of diversification and macroevolution, computing distances from allelic and nucleotide data, reading nucleotide sequences, and several […]

PSIKO v2 – Infer Population Stratification on various levels in GWAS

 Genetics & Pedigree 3 views Comments Off on PSIKO v2 – Infer Population Stratification on various levels in GWAS
Jul 142015
 
PSIKO v2 - Infer Population Stratification on various levels in GWAS

PSIKO v2 :: DESCRIPTION PSIKO (Population Structure Inference using Kernel-pca and Optimisation) is a software tool written in C++ for quick and accurate estimation of individual ancestry coefficients of a dataset exhibiting population structure. ::DEVELOPER The UEA Computational Biology Laboratory at the University of East Anglia (UEA) :: SCREENSHOTS N/A :: REQUIREMENTS Linux g++ :: DOWNLOAD […]