spkTools 1.43.0 – Collection of Functions to Analyze Microarray Spike-in data

spkTools 1.43.0

:: DESCRIPTION

spkTools contains functions that can be used to compare expression measures on different array platforms.

::DEVELOPER

Matthew N. McCall

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • R package
  • Bioconductor

:: DOWNLOAD

 spkTools

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2008 Oct;36(17):e108. doi: 10.1093/nar/gkn430. Epub 2008 Aug 1.
Consolidated strategy for the analysis of microarray spike-in data.
McCall MN, Irizarry RA.

CBT++ – Collection of C++ Classes to Computational Biology Applications

CBT++

:: DESCRIPTION

CBT++ (Computational Biology Tools) is a collection of C++ classes intended to simplify the development of complex computational biology applications. It includes basic functionality to manipulate sequences, classes to parse common kinds of files, and implementations of various sequence analysis algorithms.

::DEVELOPER

Human Genome Sequencing Center, Baylor College of Medicine

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows  / Linux / MacOsX
  • C++ Compiler

:: DOWNLOAD

 CBT++

:: MORE INFORMATION

GiRaF 1.0.2 – Find Reassortments in Collections of Influenza Genome Sequences

GiRaF 1.0.2

:: DESCRIPTION

GiRaF (Graph-incompatibility-based Reassortment Finder) is a computational tool for identification of reassortments in influenza viruses from sequence databases of isolates.

::DEVELOPER

Kingsford Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ WIndows/MacOsX
  • Perl

:: DOWNLOAD

 GiRaF

:: MORE INFORMATION

Citation

Niranjan Nagarajan and Carl Kingsford.
GiRaF: robust, computational identification of influenza reassortments via graph mining,
Nuc. Acids Res. 39(6):e34 (2011).

PgSA 1.2 – Index allowing Queries for a collection of Sequencing Reads

PgSA 1.2

:: DESCRIPTION

PgSA (Pseudogenome Suffix Array) is a compact index for collections of reads from sequencing. It allows to ask for presence of k-mers in the reads.

::DEVELOPER

REFRESH Bioinformatics Group

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 PgSA

:: MORE INFORMATION

Citation

PLoS One. 2015 Jul 16;10(7):e0133198. doi: 10.1371/journal.pone.0133198. eCollection 2015.
Indexing Arbitrary-Length k-Mers in Sequencing Reads.
Kowalski T, Grabowski S, Deorowicz S.

Sequedex 1.0.23 – Classifies DNA Sequences by Analyzing Collections of Sequences

Sequedex 1.0.23

:: DESCRIPTION

Sequedex classifies DNA sequences by analyzing collections of sequences in new ways.

::DEVELOPER

The Sequedex Team at Los Alamos National Laboratory

:: SCREENSHOTS

Sequedex

:: REQUIREMENTS

  • Linux/ MacOsX/Windows
  • Java
  • Python
  • Biopython

:: DOWNLOAD

 Sequedex

:: MORE INFORMATION

Citation

Joel Berendzen et al.
Rapid phylogenetic and functional classification of short genomic fragments with signature peptides
BMC Research Notes 2012, 5:460 doi:10.1186/1756-0500-5-460

phylotree 1.0.0 – Collection of programs for Cophylogeny Testing

phylotree 1.0.0

:: DESCRIPTION

phylotree is a collection of programs for cophylogeny testing

::DEVELOPER

Collaboratory in Computing for Bioinformatics and Biomedical Research

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 phylotree

:: MORE INFORMATION

Citation

Front Neurosci. 2010 Aug 3;4. pii: 47. doi: 10.3389/fnins.2010.00047. eCollection 2010.
Statistical phylogenetic tree analysis using differences of means.
Arnaoudova E, Haws DC, Huggins P, Jaromczyk JW, Moore N, Schardl CL, Yoshida R.

Cluster 1.3 – Build Collections of Interacting Items

Cluster 1.3

:: DESCRIPTION

Cluster is a simple unix C++ program that builds collections of interacting items from records containing interacting pairs or larger fragments. It is part of the algorithm used in Reduce to find H-bond “cliques”

::DEVELOPER

Richardson Lab

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Linux/ MacOsX/SGI-irix/Sun-SPARC

:: DOWNLOAD

Cluster

:: MORE INFORMATION

Cluster is free software available under the terms of its own BSD-style license.