BIU 2.3.7 – Bioinformatic Utility Library

BIU 2.3.7

:: DESCRIPTION

BIU (Bioinformatic Utility Library) is a C++ programming library provides a classes and functions often used in the bioinformatics context. It collects data structures and class hierarchies for biomolecule modelling and general usefull functionalities as program parameter parsing, string conversions, etc.

::DEVELOPER

Chair for Bioinformatics Freiburg

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 BIU

:: MORE INFORMATION

DendroUPGMA 201410 – A Dendrogram Construction Utility

DendroUPGMA 201410

:: DESCRIPTION

Use DendroUPGMA to create a dendrogram from (a) a set of variables, (b) a similarity matrix or (c) a distance matrix. The program calculates a similarity matrix (only for option a), transforms similarity coefficients into distances and makes a clustering using the Unweighted Pair Group Method with Arithmetic mean (UPGMA) algorithm.

::DEVELOPER

P. Puigbo, Ph.D.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

S. Garcia-Vallve, J. Palau and A. Romeu (1999)
Horizontal gene transfer in glycosyl hydrolases inferred from codon usage in Escherichia coli and Bacillus subtilis.
Molecular Biology and Evolution 9:1125-1134.

Mass-Up 1.0.9 – Mass Spectrometry Utility for Proteomics

Mass-Up 1.0.9

:: DESCRIPTION

Mass-Up is an open-source mass spectrometry software for proteomics designed to support the preprocessing and analysis of MALDI-TOF mass spectrometry data.

::DEVELOPER

The SING research group

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac OsX / Linux
  • Java

:: DOWNLOAD

 Mass-Up

:: MORE INFORMATION

Citation:

Mass-Up: an all-in-one open software application for MALDI-TOF mass spectrometry knowledge discovery.
López-Fernández H, Santos HM, Capelo JL, Fdez-Riverola F, Glez-Peña D, Reboiro-Jato M.
BMC Bioinformatics. 2015 Oct 5;16(1):318. doi: 10.1186/s12859-015-0752-4.

PEANUT 1.3.7 – The ParallEl AligNment UTility

PEANUT 1.3.7

:: DESCRIPTION

PEANUT is a read mapper for DNA or RNA sequence reads. Read mapping is the process of aligning biological DNA or RNA sequencing reads to a known reference genome.

::DEVELOPER

Johannes Köster

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Python

:: DOWNLOAD

  PEANUT

:: MORE INFORMATION

Citation

Köster J, Rahmann S (2014).
Massively parallel read mapping on GPUs with the q-group index and PEANUT.
PeerJ 2:e606 http://dx.doi.org/10.7717/peerj.606

GOBU 0.999 – Gene Ontology Browsing Utility

GOBU 0.999

:: DESCRIPTION

GOBU (Gene Ontology Browsing Utility) is a browsing and manipulating tool for Post-Pipeline genetic data, especially useful for data with GO annotations.

::DEVELOPER

Wen-Dar Lin

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • Java

:: DOWNLOAD

 GOBU

:: MORE INFORMATION

Citation

Lin WD, Chen YC, Ho JM, Hsiao CD.
GOBU: Toward an Integration Interface for Biological Objects.
Journal of Information Science and Engineering. 2006 22(1):19-29.

MCMCSALUT 1.0 – Markov Chain Monte Carlo Sequence Alignment Utility

MCMCSALUT 1.0

:: DESCRIPTION

MCMCSALUT is a program for the joint sampling of alignments and mutation parameter values for given DNA sequences.

::DEVELOPER

Dirk Metzler

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows/MacOsX
  • C++ Compiler

:: DOWNLOAD

 MCMCSALUT

:: MORE INFORMATION

Citation

Bioinformatics. 2003 Mar 1;19(4):490-9.
Statistical alignment based on fragment insertion and deletion models.
Metzler D.

SCX Prediction Utility 2.2.3994 – Strong Cation Exchange Elution Time Prediction Utility

SCX Prediction Utility 2.2.3994

:: DESCRIPTION

The SCX Prediction Utility can be used to compute the predicted strong cation exchange (SCX) fraction (on a 0 to 1 scale) in which a given peptide will appear. The software reads the peptides from a text file containing one peptide sequence on each line. The output file includes the peptide sequence plus the predicted SCX elution time value, using a normalized elution time scale of 0 to 1.

::DEVELOPER

Matthew Monroe @Biological MS Data and Software Distribution Center , Pacific Northwest National Laboratory

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows
  • Microsoft NET Framework 3.5 sp1

:: DOWNLOAD

 SCX Prediction Utility

:: MORE INFORMATION

bwtool 1.0 gamma – Utility for BigWig files

bwtool 1.0 gamma

:: DESCRIPTION

bwtool is a command-line utility for bigWig files. BigWig files are a compressed, indexed, binary format for genome-wide signal data for calculations (e.g. GC percent) or experiments (e.g. ChIP-seq/RNA-seq read depth).

::DEVELOPER

Pedro A. Ortega

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 bwtool 

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Jun 1;30(11):1618-9. doi: 10.1093/bioinformatics/btu056. Epub 2014 Jan 30.
bwtool: a tool for bigWig files.
Pohl A, Beato M.

eGATU – easy Genome Annotation Transfer Utility

eGATU

:: DESCRIPTION

eGATU (easy Genome Annotation Transfer Utility) is a light application modelled on GATU. It allows users to transfer annotations to an input genome without having to specify a reference.

::DEVELOPER

the Upton lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Java

:: DOWNLOAD

eGATU

:: MORE INFORMATION

SUP 20110711 – SLINK/FastLINK Utility Program

SUP 20110711

:: DESCRIPTION

SUP is an extension to SLINK to allow a larger number of marker loci to be simulated in pedigrees conditional on trait values and in linkage equilibrium or disequilibrium with a trait locus.

::DEVELOPER

Mathieu Lemire

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

 SUP

:: MORE INFORMATION

Citation

SUP: an extension to SLINK to allow a larger number of marker loci to be simulated in pedigrees conditional on trait values.
Lemire M.
BMC Genet. 2006 Jul 3;7:40.