Clann 4.2.4 – Construct Phylogenetic Supertrees

Clann 4.2.4

:: DESCRIPTION

Clann (the Irish word for “family”), is a free software program designed and written by Chris Creevey at the Bioinformatics and Pharmacogenomics Laboratory at NUI Maynooth. The purpose of the program is to implement methods of determining the optimal phylogenetic supertree, given a set of input source trees.

::DEVELOPER

McInerney lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOS

:: DOWNLOAD

Clann

:: MORE INFORMATION

Citation:

Creevey C. J. and McInerney, J. O. 2005
Clann: Investigating phylogenetic information through supertree analyses.
Bioinformatics 21 (3): 390-2.

Graph 1.0 – Constructs, Visualizes and Modifies Graphs

Graph 1.0

:: DESCRIPTION

Graph constructs, visualizes and modifies graphs as well as calculates measures and layouts

::DEVELOPER

The Microsoft Research – University of Trento Centre for Computational and Systems Biology

:: SCREENSHOTS

Graph

:: REQUIREMENTS

  • Windows
  • .NET Framework

:: DOWNLOAD

 Graph

:: MORE INFORMATION

Citation

Roberto Valentini, Ferenc Jordan.
COSBILab Graph: the network analysis module of COSBILab Environmental Modelling and Software, 25:886-888, 2010

CSI – Construct Confidence set of Markers within prespecified Genetic Distance from the Disease Locus

CSI

:: DESCRIPTION

CSI (confidence set inference) uses affected sib pairs data and relative risks to construct a confidence set of markers within a prespecified genetic distance from the disease locus.

::DEVELOPER

Statistical Genetics and Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 CSI

:: MORE INFORMATION

Citation

Papachristou, C., Lin, S. (2006)
Microsatellites Versus Single-Nucleotide Polymorphisms in Confidence Interval Estimation of Disease Loci.
Genetic Epidemiology, 30, 3-17.

Assemble2 2.3 – Construct & Study RNA Architectures

Assemble2 2.3

:: DESCRIPTION

Assemble proposes an intuitive graphical interface to study and construct complex three-dimensional RNA structures. When an RNA tertiary structure is opened with Assemble, it is automatically annotated with a secondary structure definition. This secondary structure can be used as a map to analyze the original tertiary structure. Using a secondary structure definition, Assemble can also produce a first draft of a 3D Model. Then the construction process can be pursued “by hand” using several widgets.

::DEVELOPER

Dr. Fabrice Jossinet at the laboratory of Pr. Eric Westhof

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • Java

:: DOWNLOAD

Assemble

:: MORE INFORMATION

Citation

Assemble: an interactive graphical tool to analyze and build RNA architectures at the 2D and 3D levels
Fabrice Jossinet; Thomas E Ludwig; Eric Westhof
Bioinformatics 2010; doi: 10.1093/bioinformatics/btq321

OpenGrowth 0.43 – Construct de novo Ligands for Protein

OpenGrowth 0.43

:: DESCRIPTION

OpenGrowth is a research program which grows new ligands in proteins by connecting small organic fragments.

::DEVELOPER

The Shakhnovich Biophysics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • MacOsX / Linux

:: DOWNLOAD

 OpenGrowth

:: MORE INFORMATION

Citation

OpenGrowth: An Automated and Rational Algorithm for Finding New Protein Ligands.
Chéron N, Jasty N, Shakhnovich EI.
J Med Chem. 2015 Sep 23

RNAlocmin 2.0 – Finds local Minima of RNA + Constructs Barrier Tree

RNAlocmin 2.0

:: DESCRIPTION

The program RNAlocmin reads secondary structures to RNA sequence provided in file seq.txt (can be altered with “-s” option) and search for a local minima by performing a gradient walk.

::DEVELOPER

Marcel Kucharík at Theoretical Biochemistry Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • ViennaRNA

:: DOWNLOAD

 RNAlocmin

:: MORE INFORMATION

Cri-Map 2.4 – Construct Multilocus Linkage Map

Cri-Map 2.4

:: DESCRIPTION

CRI-MAP‘s purpose is to allow rapid, largely automated construction of multilocus linkage maps (and facilitate the attendant tasks of assessing support relative to alternative locus orders, generating LOD tables, and detecting data errors). Although originally designed to handle codominant loci (e.g. RFLPs) scored on pedigrees “without missing individuals”, such as CEPH or nuclear families, it can now (with some caveats described below) be used on general pedigrees, and some disease loci.

::DEVELOPER

Matise Laboratory of Computational Genetics.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows wity Cygwin /MacOsX
  • GCC
:: DOWNLOAD

  CRI-MAP

:: MORE INFORMATION

Citation

Hum Hered. 1995 Mar-Apr;45(2):103-16.
Parallel computation of genetic likelihoods using CRI-MAP, PVM, and a network of distributed workstations.
Matise TC, Schroeder MD, Chiarulli DM, Weeks DE.

REMO 2.0 – Construct Full-atom Protein Models from C-alpha Traces

REMO 2.0

 

:: DESCRIPTION

REMO is a multifunctional program for constructing full-atom protein models from C-alpha traces by optimizing the backbone hydrogen-bonding networks. It gives options to choose models which are close to a given template or have more hydrogen-bonds. It has also options to build hydrogen atoms and side chain heavy atoms. The bond length and bond angle parameters are taken from CHARMM22.

::DEVELOPER

Yang Zhang’s Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / Mac OsX
  • Perl

:: DOWNLOAD

 REMO

:: MORE INFORMATION

Citation

Yunqi Li and Yang Zhang.
REMO: A new protocol to refine full atomic protein models from C-alpha traces by optimizing hydrogen-bonding networks.
Proteins, 2009, 76: 665-676

mincut-supertree – Construct Supertree

mincut-supertree

:: DESCRIPTION

Supertree is an experimental command line program for constructing supertrees.

mincut-supertree is a C++ program to compute modified mincut supertrees

::DEVELOPER

Professor Rod Page

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 mincut-supertree

:: MORE INFORMATION

Citation

Page, R.D.
Modified mincut supertrees.
WABI ’02 Proceedings of the Second International Workshop on Algorithms in Bioinformatics

E-RNAi 3.2 – Design Optimized RNAi Constructs

E-RNAi 3.2

:: DESCRIPTION

E-RNAi is a tool for the design and evaluation of RNAi reagents for a variety of species. It can be used to design and evaluate long dsRNAs (including esiRNAs) as well as siRNAs.

::DEVELOPER

E-RNAi team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser 

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

E-RNAi: a web application for the multi-species design of RNAi reagents–2010 update.
Thomas Horn; Michael Boutros
Nucl. Acids Res. (2010) 38 (suppl 2): W332-W339. doi: 10.1093/nar/gkq317