PICA – Genotype-phenotype data Mining software

PICA

:: DESCRIPTION

PICA (Phenotype Investigation with Classification Algorithms) is a Python framework for testing genotype-phenotype association algorithms.

::DEVELOPER

CUBE – Bioinformatics and Computational Systems Biology, University of Vienna

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 PICA

:: MORE INFORMATION

Citation:

Bioinformatics. 2010 Aug 1;26(15):1834-40. Epub 2010 Jun 6.
Efficient learning of microbial genotype-phenotype association rules.
MacDonald NJ, Beiko RG.

BioBlender 1.0 – Software built on the Open-source 3D Modeling software Blender

BioBlender 1.0

:: DESCRIPTION

BioBlender is a open source viewer that includes features for morphing proteins and visualization of lipophilic and electrostatic potentials.

::DEVELOPER

the SciVis Group of the Institute of Clinical Physiology – CNR, Italy.

:: SCREENSHOTS

BioBlender

:: REQUIREMENTS

  • Windows / MacOsX /  Linux

:: DOWNLOAD

 BioBlender

:: MORE INFORMATION

Citation

Andrei R.M. et al.
Intuitive representation of surface properties of biomolecules using BioBlender.
BMC Bioinformatics 2012, 13(Suppl 4):S16. Published: 28 March 2012

Network 5.011 – Phylogenetic Network Software

Network 5.011

:: DESCRIPTION

Network is used to reconstruct phylogenetic networks and trees, infer ancestral types and potential types, evolutionary branchings and variants, and to estimate datings. Network generates evolutionary trees and networks from genetic, linguistic, and other data. Network can then provide age estimates for any ancestor in the tree.

::DEVELOPER

Fluxus Technology Ltd

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 Network

:: MORE INFORMATION

Mason 0.1.2 – Read Simulator software for Illumina, 454 and Sanger reads

Mason 0.1.2

:: DESCRIPTION

Mason is a read simulator software for Illumina, 454 and Sanger reads. Its features include position specific error rates and base quality values. For Illumina reads, we give a comprehensive analysis with empirical data for the error and quality model. For the other technologies, we use models from the literature. It has been written with performance in mind and can sample reads from large genomes.

::DEVELOPER

Manuel Holtgrewe

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX /Windows

:: DOWNLOAD

 Mason

:: MORE INFORMATION

Citation

Holtgrewe, M. (2010).
Mason – a read simulator for second generation sequencing data.
Technical Report TR-B-10-06, Institut für Mathematik und Informatik, Freie Universität Berlin.

newDNA-Prot – DNA Binding Protein Predict Software

newDNA-Prot

:: DESCRIPTION

newDNA-Prot will predict the DNA-binding proteins when input a protein sequence (Fasta format).

::DEVELOPER

newDNA-Prot team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows
  • fortran-windows

:: DOWNLOAD

newDNA-Prot

:: MORE INFORMATION

Citation

newDNA-Prot: Prediction of DNA-binding proteins by employing support vector machine and a comprehensive sequence representation.
Zhang Y, Xu J, Zheng W, Zhang C, Qiu X, Chen K, Ruan J.
Comput Biol Chem. 2014 Oct;52:51-9. doi: 10.1016/j.compbiolchem.2014.09.002.

EuGene 1.4.0 – Gene Optimisation Software

EuGene  1.4.0

:: DESCRIPTION

EuGene is a gene redesign software. It allows opening and parsing genome files, loading genes into a workspace, and redesign the genes according to many redesign methodologies such as enhancing codon usage, codon context, GC content, hidden stop codons, repeated codons or nucleotides, harmonizing genes to other host species, avoiding deleterious sequences, among others. EuGene is free and auto-updates so you can always be up to the latest features and corrections.

::DEVELOPER

UA.PT Bioinformatics

:: SCREENSHOTS

EuGene

::REQUIREMENTS

  • Linux/ Windows/MacOsX
  • Java

:: DOWNLOAD

 EuGene

:: MORE INFORMATION

Citation

Bioinformatics. 2016 Apr 1;32(7):1120. doi: 10.1093/bioinformatics/btw063. Epub 2016 Mar 7.
EuGene: maximizing synthetic gene design for heterologous expression.
Gaspar P, Luís Oliveira J, Frommlet J, Santos MA, Moura G.

Bioinformatics. 2012 Oct 15;28(20):2683-4. doi: 10.1093/bioinformatics/bts465. Epub 2012 Jul 30.
EuGene: maximizing synthetic gene design for heterologous expression.
Gaspar P, Oliveira JL, Frommlet J, Santos MA, Moura G.

FastPval – Fast Two Stage P-value Computation Software

FastPval

:: DESCRIPTION

FastPval is a two stage p-value computation software which compute the empirical p-value by two stage ranking strategy, it can produce very low P-value based on huge dataset. This fast and powerful tool takes advantage of a delicate cutoff which separate the exactly significant area. Compared to the traditional ranking method, Tspvc has a good time efficiency, lower memory consuming and tiny storage spaces with high accuracy.

::DEVELOPER

JJWang Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOS
  • Java

:: DOWNLOAD

FastPval

:: MORE INFORMATION

Citation

Mulin Jun Li, Pak Chung Sham, and Junwen Wang
FastPval: a fast and memory efficient program to calculate very low P-values from empirical distribution.
Bioinformatics. 2010 Nov 15;26(22):2897-9. Epub 2010 Sep 21.

Bosque 2.0.2 – Phylogenetic Analysis Software

Bosque 2.0.2

:: DESCRIPTION

Bosque is a distributed software environment oriented to manage the computational resources involved in typical phylogenetic analyses. Bosque has been implemented as a client-server application where the server  can execute installed phylogenetic programs (Phylip, PhyML, TreePuzzle, Muscle) and the client manages the results on a local relational database, although it can also execute phylogenetic programs locally, useful when no server is available. The client also performs the graphical visualisation and edition of trees and alignments, providing an environment for the analyses, from the integration of sequences to the printing of a final tree.

::DEVELOPER

Millenium Institute of Oceanography

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX / Linux

:: DOWNLOAD

Bosque

:: MORE INFORMATION

Citation:

Ramírez-Flandes S. & O. Ulloa(2008).
Bosque: Integrated phylogenetic analysis software.
Bioinformatics 24(21):2539-2541; doi: 10.1093/bioinformatics/btn466

GenomeTools 1.5.8 – Genome Analysis Software

GenomeTools 1.5.8

:: DESCRIPTION

GenomeTools genome analysis system is a free collection of bioinformatics tools (in the realm of genome informatics) combined into a single binary named gt.

::DEVELOPER

RESEARCH GROUP FOR GENOME INFORMATICS ,Center for Bioinformatics, University of Hamburg

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX /Windows with Cygwin

:: DOWNLOAD

GenomeTools ; for Windows

:: MORE INFORMATION

The GenomeTools distribution includes several published software tools:

  • ltrharvest, an efficient and flexible software tool for de novo detection of LTR retrotransposons.
    D. Ellinghaus, S. Kurtz, and U. Willhoeft.
    LTRharvest, a efficient and flexible software for de novo detection of LTR retrotransposons.
    BMC Bioinformatics 2008, 9:18
  • tallymer, a collection of flexible and memory-efficient programs for k-mer counting and indexing of large sequence sets.
    S. Kurtz, A. Narechania, J.C. Stein, and D. Ware.
    A new method to compute K-mer frequencies and its application to annotate large repetitive plant genomes.
    BMC Genomics 2008, 9:517
  • uniquesub, a program for computing minimum unique substrings.
    S. Gräf, F.G.G. Nielsen, S. Kurtz, M.A. Huynen, E. Birney, H. Stunnenberg, and P. Flicek.
    Optimized design and assessment of whole genome tiling arrays.
    Bioinformatics 2007, 23(13):i195–i204
  • AnnotationSketch, a library for drawing genome annotations.
    S. Steinbiss, G. Gremme, C. Schärfer, M. Mader and S. Kurtz.
    AnnotationSketch: a genome annotation drawing library.
    Bioinformatics 2009, 25(4):533–534
  • ltrdigest, a software tool for automated annotation of internal features of LTR retrotransposons.
    S. Steinbiss, U. Willhoeft, G. Gremme and S. Kurtz.
    Fine-grained annotation and classification of de novo predicted LTR retrotransposons.
    Nucleic Acids Research 2009, 37(21):7002–7013
  • MetaGenomeThreader, a software to predict genes, such as PCS’s (predicted coding sequences) in sequences of metagenome projects.
    D.J. Schmitz-Hübsch and S. Kurtz.
    MetaGenomeThreader: A software tool for predicting genes in DNA-sequences of metagenome projects.
    In R. Daniel and W. Streit (Eds.), Metagenomics. Methods in Molecular Biology, 325–338, Humana Press, Totowa, NJ, ISBN 978-1-60761-822-5
  • GtEncseq, a compressed biosequence representation with many features.
    S. Steinbiss and S. Kurtz.
    A New Efficient Data Structure for Storage and Retrieval of Multiple Biosequences.
    IEEE/ACM Transactions on Computational Biology and Bioinformatics 2012, 9(2):345–357
  • Readjoiner, a sequence assembler based on the assembly string graph framework.
    G. Gonnella and S. Kurtz.
    Readjoiner: a fast and memory efficient string graph-based sequence assembler.
    BMC Bioinformatics 2012, 13:82

TreeView 1.6.6 / TreeView X 0.5-1 – Tree Drawing Software

TreeView 1.6.6 / TreeView X 0.5-1

:: DESCRIPTION

TreeView is a simple program for displaying phylogenies on Apple Macintosh and Windows PCs.TreeView provides a simple way to view the contents of a NEXUS, PHYLIP, Hennig86, Clustal, or other format tree file. While PAUP and MacClade have excellent tree printing facilities, there may be times you just want to view the trees without having to load the data set they were generated from. The PHYLIP package contains tree drawing programs which offer a greater variety of trees than TreeView, but are somewhat clumsy to use. The forthcoming PAUP* for Windows does not have a graphical interface, hence TreeView allows you to create publication quality trees from PAUP files, either directly, or by generating graphics files for editing by other programs.

TreeView X is an open source program to display phylogenetic trees on Linux, Unix, Mac OS X, and Windows platforms

::DEVELOPER

Professor Rod Page

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows /  Mac OsX / Linux

:: DOWNLOAD

TreeView , TreeView X

:: MORE INFORMATION

Citation

Page, R. D. M. 1996.
TREEVIEW: An application to display phylogenetic trees on personal computers.
Computer Applications in the Biosciences 12: 357-358.