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

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.

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.

Vector NTI Advance 11.5.4 – Sequence Analysis and Data Management software

Vector NTI Advance 11.5.4

:: DESCRIPTION

Vector NTI® Advance software is the most highly integrated, multifunctional desktop sequence analysis application suite available today and provides superior integration, data management, and scalability.

::DEVELOPER

Life Technologies

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac OS X with Parallels

:: DOWNLOAD

Vector NTI Advance

:: MORE INFORMATION

PeakQuant 1.5.47 – Proteomics Software Suit

PeakQuant 1.5.47

:: DESCRIPTION

PeakQuant (formerly known as Peakardt) serves as an integrated platform for several Proteomics tools and provides an easily operated graphical user interface.

::DEVELOPER

Medizinisches Proteom-Center, Medical Bioinformatics

:: SCREENSHOTS

PeakQuant

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • JRE

:: DOWNLOAD

 PeakQuant

:: MORE INFORMATION

Citation

OMICS. 2012 Sep;16(9):457-67. doi: 10.1089/omi.2011.0140. Epub 2012 Aug 21.
Find pairs: the module for protein quantification of the PeakQuant software suite.
Eisenacher M1, Kohl M, Wiese S, Hebeler R, Meyer HE, Warscheid B, Stephan C.

IOCBio 1.2.2 – Open-source Software from the Laboratory of Systems Biology

IOCBio 1.2.2

:: DESCRIPTION

The IOCBio project provides open-source software that is developed in Laboratory of Systems Biology at Institute of Cybernetics. The project is created to publish the software, this includes distributing the source codes, continuing software development, supporting users as well as attracting users to contribute to the software.

::DEVELOPER

Laboratory of Systems Biology at Institute of Cybernetics.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Python

:: DOWNLOAD

IOCBio

:: MORE INFORMATION

Citation

J Microsc. 2011 Aug;243(2):124-40. doi: 10.1111/j.1365-2818.2011.03486.x. Epub 2011 Feb 15.
Application of regularized Richardson-Lucy algorithm for deconvolution of confocal microscopy images.
Laasmaa M, Vendelin M, Peterson P.

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

Bioinformatics Group, HKU Department of Biochemistry

:: 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.

PhyML 20141029 – Phylogeny software based on the Maximum Likelihood

PhyML 20141029

:: DESCRIPTION

PhyML (Phylogenetic estimation using Maximum Likelihood) is a phylogeny software based on the maximum-likelihood principle. Early PhyML versions used a fast algorithm to perform Nearest Neighbor Interchanges (NNIs), in order to improve a reasonable starting tree topology.

PhyML Online Version

::DEVELOPER

Stéphane GuindonOlivier Gascuel

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX / Linux

:: DOWNLOAD

PhyML

:: MORE INFORMATION

Citation:

Guindon S., Dufayard J.F., Lefort V., Anisimova M., Hordijk W., Gascuel O.
New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0
Systematic Biology, 59(3):307-21, 2010.