Tag: Program

ArgusLab 4.0.1 – Molecular Modeling, Graphics & Drug Design Program

ArgusLab 4.0.1

:: DESCRIPTION

ArgusLab is a molecular modeling, graphics, and drug design program.The ArgusDock docking engine, implemented in ArgusLab4.0, approximates an exhaustive search method, with similarities to DOCK and Glide. Flexible ligand docking is possible with ArgusLab, where the ligand is described as a torsion tree and grids are constructed that overlay the binding site. Ligand’s root node (group of bonded atoms that do not have rotatable bonds) is placed on a search point in the binding site and a set of diverse and energetically favorable rotations is created. For each rotation, torsions in breadth-first order are constructed and those poses that survive the torsion search are scored. The N-lowest energy poses are retained and the final set of poses undergoes coarse minimization, re-clustering and ranking.

::DEVELOPER

Mark A. Thompson , Planaria Software LLC, Seattle, WA

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

ArgusLab

:: MORE INFORMATION

Citation

Thompson, M. A. (2004).
Molecular docking using ArgusLab, an efficient shape-based search algorithm and the AScore scoring function.
ACS meeting, Philadelphia, 172, CINF 42, PA.

Hands On Genetics 2.6 – Interactive Education Programs of Genetics

Hands On Genetics 2.6

:: DESCRIPTION

Hands On Genetics is a suite of interactive programs covering a wide range of topics in genetics.
Mendelian genetics:
SimpleGene, Mendelsim, SexLink, Punnett, GeneShare

Cytogenetics:
Meiosis

Molecular genetics:
Genetic molecules, PCR, Gelsim

Population genetics:
Popsim, Hardy-Weinberg, Fisher-Wright

::DEVELOPER

Hands On Genetics Editorial Board

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOSX

:: DOWNLOAD

Hands On Genetics

:: MORE INFORMATION

LTR_STRUC – LTR Retrotransposon Structure program

LTR_STRUC

:: DESCRIPTION

LTR_STRUC is a new data-mining program that scans nucleotide sequence files for LTR retrotransposons and analyzes any resulting hits. Input files can be in fasta or NCBI flat file format.

::DEVELOPER

McDonald Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  Contact with Vinay Mittal ( vinaykmittal@gatech.edu )

:: MORE INFORMATION

Citation:

McCarthy, E.M., and J.F. McDonald. 2003.
LTR_STRUC: A novel search and identification program for LTR retrotransposons.
Bioinformatics 19: 362-367

OSA 2.1 – Ordered Subset Analysis Program

OSA 2.1

:: DESCRIPTION

OSA (Ordered Subset Analysis Program ) allows the researcher to evaluate evidence for linkage even when heterogeneity is present in a data set. This is not an unusual occurrence when studying diseases of complex origin. Families are ranked by covariate values in order to test evidence for linkage among homogeneous subsets of families. Because families are ranked, a priori covariate cutpoints are not necessary. Covariates may include linkage evidence at other genes, environmental exposures, or biological trait values such as cholesterol, age at onset, and so on.

::DEVELOPER

Duke Molecular Physiology Institute

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 OSA

:: MORE INFORMATION

Citation

Hauser E.R., et al.
Ordered subset analysis in genetic linkage mapping of complex traits.
Genet. Epidemiol 2004;27:53-63

CDPOP 1.2.32 – Spatially-explicit Cost Distance Population Genetics program

CDPOP 1.2.32

:: DESCRIPTION

CDPOP (Cost Distance POPulations) is a spatially-explicit simulator of gene-flow in complex landscapes to explain observed population responses and provide a foundation for landscape genetics.

::DEVELOPER

the Computational Ecology Lab, The University of Montana

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOsX

:: DOWNLOAD

 CDPOP

:: MORE INFORMATION

Citation

Landguth EL, Cushman, SA (2010)
CDPOP: A spatially-explicit cost distance population genetics program.
Molecular Ecology Resources 10, 156-161

Endrov 2.23.3 – Multi-purpose Image Analysis program

Endrov 2.23.3

:: DESCRIPTION

Endrov is a multi-purpose image analysis program. It is written indepedently and designed to address many of the shortcomings of ImageJ and many commercial packages. The sofware is a framework for image analysis and data analysis, aimed towards microscopy and the needs of current research.

::DEVELOPER

HenLab

:: SCREENSHOTS

:: REQUIREMENTS

  • MacOsX / Linux / Windows

:: DOWNLOAD

 Endrov

:: MORE INFORMATION

Citation

Nat Methods. 2013 Jun;10(6):454-6. doi: 10.1038/nmeth.2478.
Endrov: an integrated platform for image analysis.
Henriksson J, Hench J, Tong YG, Johansson A, Johansson D, Bürglin TR.

LASTZ 1.04.03 – Program for Aligning DNA Sequences

LASTZ 1.04.03

:: DESCRIPTION

LASTZ is a program for aligning DNA sequences, a pairwise aligner. Originally designed to handle sequences the size of human chromosomes and from different species, it is also useful for sequences produced by NGS sequencing technologies such as Roche 454.

::DEVELOPER

Miller Lab at Penn State University Center for Comparative Genomics and Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  LASTZ

:: MORE INFORMATION

Citation:

Harris, R.S. (2007)
Improved pairwise alignment of genomic DNA.
Ph.D. Thesis, The Pennsylvania State University.

RDP 5.05 – Recombination Detection Program

RDP 5.05

:: DESCRIPTION

RDP (Recombination detection program) is software that applies a number of recombination detection and analysis algorithms. Among other novelties, this version includes four new recombination analysis methods (3SEQ, VISRD, PHYLRO and LDHAT), new tests for recombination hot-spots, a range of matrix methods for visualizing over-all patterns of recombination within datasets and recombination-aware ancestral sequence reconstruction. Complementary to a high degree of analysis flow automation, RDP also has a highly interactive and detailed graphical user interface that enables more focused hands-on cross-checking of results with a wide variety of newly implemented phylogenetic tree construction and matrix-based recombination signal visualization methods. RDP can accommodate large datasets and is capable of analyzing alignments ranging in size from 1000×10 kilobase sequences to 20×2 megabase sequences within 48 h on a desktop PC.

::DEVELOPER

Phylogenomics Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 RDP

:: MORE INFORMATION

Citation

Martin DP, Lemey P, Lott M, Moulton V, Posada D, Lefeuvre P. (2010).
RDP3: a flexible and fast computer program for analyzing recombination.
Bioinformatics 26, 2462-2463

BKChem 0.14.0-pre2 – Free Chemical Drawing Program

BKChem 0.14.0-pre2

:: DESCRIPTION

BKChem is a free chemical drawing program.

::DEVELOPER

written by Beda Kosata ,  currently maintained by Reinis Danne.

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

BKChem

:: MORE INFORMATION

BKChem is free software.

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