Tag: Program

BSMAP 2.90 – Whole Genome Bisulfite Sequence MAPping program

BSMAP 2.90

:: DESCRIPTION

BSMAP（Bisulfite Sequence Mapping Program）is a short reads mapping software for bisulfite sequencing reads. Bisulfite treatment converts unmethylated Cytosines into Uracils (sequenced as Thymine) and leave methylated Cytosines unchanged, hence provides a way to study DNA cytosine methylation at single nucleotide resolution. BSMAP aligns the Ts in the reads to both Cs and Ts in the reference.

::DEVELOPER

Li Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

BSMAP

:: MORE INFORMATION

Citation:

BSMAP: whole genome bisulfite sequence MAPping program.
Xi Y, Li W.
BMC Bioinformatics. 2009 Jul 27;10:232. doi: 10.1186/1471-2105-10-232.

Bioinformatics. 2012 Feb 1;28(3):430-2. doi: 10.1093/bioinformatics/btr668. Epub 2011 Dec 6.
RRBSMAP: a fast, accurate and user-friendly alignment tool for reduced representation bisulfite sequencing.
Xi Y, Bock C, Müller F, Sun D, Meissner A, Li W.

BRAGI 20091106 – A Protein Visualization and Modeling Program

BRAGI 20091106

:: DESCRIPTION

BRAGI is a well-established package for viewing and modeling of three-dimensional (3D) structures of biological macromolecules.BRAGI enables you to view and explore the three-dimensional (3D) structure of any macromolecule. You can explore proteins, DNA, RNA, carbohydrates, and complexes, such as between transcriptional regulatory proteins and DNA, or enzymes and drugs.

::DEVELOPER

BRAGI Team

:: SCREENSHOTS

BRAGI

:: REQUIREMENTS

  • Windows / Linux

:: DOWNLOAD

 BRAGI

:: MORE INFORMATION

Citation

BRAGI: linking and visualization of database information in a 3D viewer and modeling tool.
Reichelt J, Dieterich G, Kvesic M, Schomburg D, Heinz DW.
Bioinformatics. 2005 Apr 1;21(7):1291-3. Epub 2004 Nov 16.

NJplot 2.4 – Phylogenetic Tree Drawing Program

NJplot 2.4

:: DESCRIPTION

NJplot is a tree drawing program able to draw any phylogenetic tree expressed in the Newick phylogenetic tree format (e.g., the format used by the PHYLIP package). NJplot is especially convenient for rooting the unrooted trees obtained from parsimony, distance or maximum likelihood tree-building methods.

::DEVELOPER

PRABI-Doua

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOSX

:: DOWNLOAD

NJplot

:: MORE INFORMATION

Citation

Perrière, G. and Gouy, M. (1996)
WWW-Query: An on-line retrieval system for biological sequence banks.
Biochimie, 78, 364-369.

Vanilla 1.2 – Programs to Access Features in PAL

Vanilla 1.2

:: DESCRIPTION

Vanilla is a collection of command line programs written in Java to access some selected features in PAL, a Java library for molecular evolution and phylogenetics (see http://www.cebl.auckland.ac.nz/pal-project/ for details on PAL). Note that Vanilla does not provide all functionality available in PAL.

::DEVELOPER

Strimmer Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Java

:: DOWNLOAD

Vanilla

:: MORE INFORMATION

Citation

Drummond, A., and K. Strimmer. 2001.
PAL: An object-oriented programming library for molecular evolution and phylogenetics.
Bioinformatics 17: 662-663.

YASARA 19.12.14 – Molecular Graphics, Modeling & Simulation program

YASARA 19.12.14

:: DESCRIPTION

YASARA (Yet Another Scientific Artificial Reality Application)is a molecular-graphics, -modeling and -simulation program.With an intuitive user interface, photorealistic graphics and support for affordable shutter glasses, autostereoscopic displays and input devices, YASARA creates a new level of interaction with the ‘artificial reality’, that allows you to focus on your goal and forget about the details of the program.

YASARA View is available for free and contains the basic functions you need to explore a macromolecular structure interactively, comparable to other molecule viewers.

YASARA Model contains YASARA View and adds all the functions you need to explore, analyze and model small and macromolecules in a production environment. This includes many features you often miss: unlimited undo/redo, macro recorder, quad-buffered stereo with shutter glasses or the DTI virtual window .

YASARA Dynamics contains YASARA Model and adds support for molecular simulations.

YASARA Structure contains YASARA Dynamics and adds all the functions needed to predict and validate macromolecular structures, including ligand docking and highly accurate force fields with knowledge-based potentials, and an optional module for NMR structure determination.

::DEVELOPER

YASARA Biosciences

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac /  Linux

:: DOWNLOAD

YASARA

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Jul 4. pii: btu426.
YASARA View – molecular graphics for all devices – from smartphones to workstations.
Krieger E1, Vriend G

Bioinformatics. 2002 Feb;18(2):315-8.
Models@Home: distributed computing in bioinformatics using a screensaver based approach.
Krieger E, Vriend G.

phyl_util – Phylogenetic Utility Programs

phyl_util

:: DESCRIPTION

Phylogenetic Utility Programs includes programs to aid in the summary of the posterior distribution of phylogenetic trees from the program MrBayes are provided.The first program, post_prob, will tabulate the percentage of times each tree topology appears in the posterior distribution output by MrBayes, thus providing posterior probabilities for each tree topology. The second program, post_root, will tabulate the percentage of times each possible root position appears in the posterior distribution output by MrBayes, thus providing posterior probabities for each root.

::DEVELOPER

Laura S. Kubatko

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler
  • R package

:: DOWNLOAD

 Phylogenetic Utility Programs

:: MORE INFORMATION

RadCon 1.1.6 – Phylogenetic Tree Consensus & Comparison Program

RadCon 1.1.6

:: DESCRIPTION

RadCon is a phylogenetic tree consensus and comparison program for Macs (OS 7.5 – 9).Implemented methods include the strict reduced consensus method, leaf stability, cladistic information content, double decay analysis and matrix representation with parsimony.

::DEVELOPER

RadCon team

:: SCREENSHOTS

:: REQUIREMENTS

  • Mac(OS 7.5 – 9)

:: DOWNLOAD

 RadCon

:: MORE INFORMATION

Citation

Joseph L. Thorley and Roderic D. M. Page
RadCon: phylogenetic tree comparison and consensus
Bioinformatics (2000) 16 (5): 486-487.

EvolveAGene 4.02 – DNA Coding Sequence Evolution Simulation program

EvolveAGene 4.02

:: DESCRIPTION

EvolveAGene is a DNA coding sequence evolution simulation program.

::DEVELOPER

Barry G. Hall

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX

:: DOWNLOAD

  EvolveAGene

:: MORE INFORMATION

Citation

Mol Biol Evol. 2008 Apr;25(4):688-95. doi: 10.1093/molbev/msn008. Epub 2008 Jan 12.
Simulating DNA coding sequence evolution with EvolveAGene 3.
Hall BG.

Parsimonator 1.02 – Fast open-source Parsimony program

Parsimonator 1.02

:: DESCRIPTION

Parsimonator is a no-frills light-weight implementation for building starting trees under parsimony for RAxML-Light

::DEVELOPER

the Exelixis Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  Parsimonator

:: MORE INFORMATION

MAP 20121108 – A de novo Metagenomic Assembly program for Shotgun DNA reads

MAP 20121108

:: DESCRIPTION

MAP (Metagenomic Assembly program) is a de novo assembly approach and its implementation based on an improved Overlap/Layout/Consensus (OLC) strategy incorporated with several special algorithms.MAP uses the mate pair information, resulting in being more applicable to shotgun DNA reads (recommended as > 200 bp) currently widely-used in metagenome projects. Results of extensive tests on simulated data show that MAP can be superior to both Celera and Phrap for typical longer reads by Sanger sequencing, as well as has an evident advantage over Celera, Newbler, and the newest Genovo, for typical shorter reads by 454 sequencing.

::DEVELOPER

ZhuLab, Peking Uiniversity, Beijing

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

MAP

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Jun 1;28(11):1455-62. Epub 2012 Apr 11.
A de novo metagenomic assembly program for shotgun DNA reads.
Lai B, Ding R, Li Y, Duan L, Zhu H.