PSGInfer 1.2.1 – Inference of Alternative Splicing from RNA-Seq data with probabilistic Splice Graphs

PSGInfer 1.2.1

:: DESCRIPTION

PSGInfer (Probabilistic Splice Graph Inference) analyzes RNA-Seq data with probabilistic splice graph models of alternative RNA processing (transcription initiation, splicing, and polyadenylation).

::DEVELOPER

Laura H. LeGault , Colin Dewey

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

PSGInfer

:: MORE INFORMATION

Citation

Laura H. LeGault and Colin N. Dewey. (2013)
Inference of alternative splicing from RNA-Seq data with probabilistic splice graphs.
Bioinformatics. 29(18):2300-2310.

CCLasso – Correlation Inference for Compositional Data through Lasso

CCLasso

:: DESCRIPTION

CCLasso is a novel method based on least squares with ℓ1 penalty to infer the correlation network for latent variables of compositional data from metagenomic data

::DEVELOPER

Fang Huaying (hyfang@pku.edu.cn) , Minghua Deng

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • R

:: DOWNLOAD

 CCLasso

:: MORE INFORMATION

Citation

CCLasso: Correlation Inference for Compositional Data through Lasso.
Fang H, Huang C, Zhao H, Deng M.
Bioinformatics. 2015 Jun 4. pii: btv349.

QuasiRecomb 1.2 – Inference of Quasispecies subjected to Recombination

QuasiRecomb 1.2

:: DESCRIPTION

QuasiRecomb is a software of Inference of Quasispecies subjected to Recombination.RNA viruses are present in a single host as a population of different but related strains. This population, shaped by the combination of genetic change and selection, is called quasispecies. Genetic change is due to both point mutations and recombination events. We present a jumping hidden Markov model that describes the generation of the viral quasispecies and a method to infer its parameters by analysing next generation sequencing data. We offer an implementation of the EM algorithm to find maximum a posteriori estimates of the model parameters and a method to estimate the distribution of viral strains in the quasispecies. The model is validated on simulated data, showing the advantage of explicitly taking the recombination process into account, and tested by applying to reads obtained from experimental HIV samples.

::DEVELOPER

the Computational Biology Group (CBG)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Mac /  Linux
  • Java

:: DOWNLOAD

 QuasiRecomb

:: MORE INFORMATION

Citation

J Comput Biol. 2013 Feb;20(2):113-23. doi: 10.1089/cmb.2012.0232.
Probabilistic inference of viral quasispecies subject to recombination.
Töpfer A, Zagordi O, Prabhakaran S, Roth V, Halperin E, Beerenwinkel N.

REDUCE 1.0 – Optimal Design of Gene Knock-out (KO) for the purpose of Gene Regulatory Network (GRN) Inference

REDUCE 1.0

:: DESCRIPTION

REDUCE (REDuction of UnCertain Edges) is an algorithm for finding the optimal gene KO experiment for inferring directed graphs (digraphs) of gene regulatory network (GRN).

:: DEVELOPER

Chemical and Biological Systems Engineering Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / windows/ MacOsX
  • MatLab

:: DOWNLOAD

 REDUCE

:: MORE INFORMATION

Citation

Optimal design of gene knock-out experiments for gene regulatory network inference.
Ud-Dean SM, Gunawan R.
Bioinformatics. 2015 Nov 14. pii: btv672

Hi-Jack – Pathway-based Inference of Host-pathogen Interactions

Hi-Jack

:: DESCRIPTION

Hi-Jack, a novel computational framework, for inferring pathway-based interactions between a host and a pathogen that relies on the idea of metabolite hijacking.

::DEVELOPER

InfoCloud Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • C++ Compiler

:: DOWNLOAD

Hi-Jack

:: MORE INFORMATION

Citation:

Hi-Jack: A novel computational framework for pathway-based inference of host-pathogen interactions.
Kleftogiannis D, Wong L, Archer JA, Kalnis P.
Bioinformatics. 2015 Mar 9. pii: btv138

Hieranoid 2.0 – Hierarchical Orthology Inference

Hieranoid 2.0

:: DESCRIPTION

Hieranoid is an orthology inference method using a hierarchical approach. Hieranoid performs pairwise orthology analysis using InParanoid at each node in a guide tree as it progresses from its leaves to the root. This concept reduces the total runtime complexity from a quadratic to a linear function of the number of species.

::DEVELOPER

Sonnhammer Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

Hieranoid

:: MORE INFORMATION

Citation

J Mol Biol. 2013 Jun 12;425(11):2072-2081. doi: 10.1016/j.jmb.2013.02.018.
Hieranoid: hierarchical orthology inference.
Schreiber F, Sonnhammer ELL.

ANAT 20180308 – Inference and Analysis of Functional Networks of Proteins

ANAT 20180308

:: DESCRIPTION

ANAT (Advanced Network Analysis Tool) , is an all-in-one resource that provides access to up-to-date large-scale physical association data in several organisms, advanced algorithms for network reconstruction, and a number of tools for exploring and evaluating the obtained network models

::DEVELOPER

Prof. Roded Sharan

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 ANAT

:: MORE INFORMATION

Citation

ANAT: A Tool for Constructing and Analyzing Functional Protein Networks.
N. Yosef, E. Zalckvar, A. D. Rubinstein, M. Homilius, N. Atias, L. Vardi, I. Berman, H. Zur, A. Kimchi, E. Ruppin and R. Sharan
Sci. Signal. 4, pl1 (2011).

TWIGS – Three-Way module Inference via Gibbs Sampling

TWIGS

:: DESCRIPTION

TWIGS is a tool for advanced analysis of three-way data (e.g., patient-gene-time in gene expression or subject-voxel-time in fMRI). TWIGS identifies both core modules that appear in multiple patients and patient-specific augmentations of these core modules that contain additional genes.

::DEVELOPER

Ron Shamir’s lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/ MacOsX
  • R

:: DOWNLOAD

 TWIGS

:: MORE INFORMATION

Citation

A hierarchical Bayesian model for flexible module discovery in three-way time-series data.
Amar D, Yekutieli D, Maron-Katz A, Hendler T, Shamir R.
Bioinformatics. 2015 Jun 15;31(12):i17-i26. doi: 10.1093/bioinformatics/btv228.

lpNet 2.18.0 – Linear Programming Model for Network Inference

lpNet 2.18.0

:: DESCRIPTION

lpNet aims at infering biological networks, in particular signaling and gene networks.

::DEVELOPER

Lars Kaderali

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • R
  • BioConductor

:: DOWNLOAD

 lpNet

:: MORE INFORMATION

Citation

lpNet: a linear programming approach to reconstruct signal transduction networks.
Matos MR, Knapp B, Kaderali L.
Bioinformatics. 2015 May 29. pii: btv327

SSA 1.0 – Inference of Maximum Likelihood Phylogenetic Trees Using a Stochastic Search Algorithm

SSA 1.0

:: DESCRIPTION

SSA is a program for inferring maximum likelihood phylogenies from DNA sequences. Two versions of the program are available: one which assumes a molecular clock and one which does not make this assumption. The method for searching the space of trees for the ML tree is based on a simulated-annealing type algorithm and is described in the reference above. The program implements Felsenstein’s F84 model of nucleotide substitution and associated sub-models. The program estimates the ML tree and branch lengths, and can optionally estimate the transversion/transversion ratio. Upon termination, the program returns the k trees of highest likelihood found during the search, where k can be set by the user.

::DEVELOPER

Laura S. Kubatko

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows

:: DOWNLOAD

 SSA

:: MORE INFORMATION

Citation

Salter, L. and D. Pearl. 2001.
Stochastic Search Strategy for Estimation of Maximum Likelihood Phylogenetic Trees,
Systematic Biology 50(1): 7-17.