SDSE 2.0 – Simulation of DNA Sequence Evolution

SDSE 2.0

:: DESCRIPTION

SDSE is an  algorithm  to  simulate  DNA  sequence  evolution  under  a  general  stochastic  model,  including  as  particular  cases  all  the  previously  used  schemes  of  nucleotide  substitution

::DEVELOPER

The group of computational genomics and bioinformatics at Granada University (Spain)

:: SCREENSHOTS

SDSE

:: REQUIREMENTS

  • DOS

:: DOWNLOAD

 SDSE

:: MORE INFORMATION

Citation:

Comput Appl Biosci. 1989 Feb;5(1):47-50.
SDSE: a software package to simulate the evolution of a pair of DNA sequences.
Oliver JL, Marín A, Medina JR.

nhPhyML – Compute Phylogenetic Trees under non Homogeneous model of DNA sequence Evolution

nhPhyML

:: DESCRIPTION

nhPhyML is a program built to compute phylogenetic trees under the non stationary, non homogeneous model of DNA sequence evolution of Galtier and Gouy (1998).

::DEVELOPER

Bastien Boussau

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  Mac OsX

:: DOWNLOAD

  nhPhyML

:: MORE INFORMATION

Citation

Efficient likelihood computations with nonreversible models of evolution.
Boussau B, Gouy M.
Syst Biol. 2006 Oct;55(5):756-68.

MySSP 1.0.3.5 – Simulation of DNA Sequence Evolution across a Phylogenetic Tree

MySSP 1.0.3.5

:: DESCRIPTION

MySSP is a program for the simulation of DNA sequence evolution across a phylogenetic tree

::DEVELOPER

Michael S. Rosenberg’s Laboratory

:: SCREENSHOTS

MySSP

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 MySSP

:: MORE INFORMATION

Citation

Rosenberg, M.S. (2005)
MySSP: Non-stationary evolutionary sequence simulation, including indels.
Evolutionary Bioinformatics Online 1:81–83

PromFD 1.0 – Predict Promoter Regions in DNA Sequences

PromFD 1.0

:: DESCRIPTION

PromFD is a computer program to recognize vertebrate RNA polymerase II promoters

::DEVELOPER

Stormo Lab in Department of Genetics, Washington University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 PromFD

:: MORE INFORMATION

Citation

Comput Appl Biosci. 1997 Feb;13(1):29-35.
PromFD 1.0: a computer program that predicts eukaryotic pol II promoters using strings and IMD matrices.
Chen QK, Hertz GZ, Stormo GD.

SRF 1.1 – Find Repeats through an analysis of the power Spectrum of a given DNA Sequence

SRF 1.1

:: DESCRIPTION

 SRF (Spectral Repeat Finder) is a program to find repeats through an analysis of the power spectrum of a given DNA sequence. By repeat we mean the repeated occurrence of a segment of N nucleotides within a DNA sequence. SRF is an ab initio technique as no prior assumptions need to be made regarding either the repeat length, its fidelity, or whether the repeats are in tandem or not

::DEVELOPER

SRF Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Bioinformatics. 2004 Jun 12;20(9):1405-12. Epub 2004 Feb 19.
Spectral Repeat Finder (SRF): identification of repetitive sequences using Fourier transformation.
Sharma D, Issac B, Raghava GP, Ramaswamy R.

Staden 2.0.0b11 – DNA Sequence Assembly , Editing and Analysis

Staden 2.0.0b11

:: DESCRIPTION

Staden is a fully developed set of DNA sequence assembly (Gap4 and Gap5), editing and analysis tools (Spin) .

::DEVELOPER

Staden Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / Mac OsX

:: DOWNLOAD

Staden

:: MORE INFORMATION

Citation

Bioinformatics. 2010 Jul 15;26(14):1699-703. doi: 10.1093/bioinformatics/btq268. Epub 2010 May 30.
Gap5–editing the billion fragment sequence assembly.
Bonfield JK1, Whitwham A.

Rodger Staden, David P. Judge and James K. Bonfield.
Analysing Sequences Using the Staden Package and EMBOSS.
Introduction to Bioinformatics. A Theoretical and Practical Approach. Eds. Stephen A. Krawetz and David D. Womble. Human Press Inc., Totawa, NJ 07512 (2003)

ACANA – Accurate and Consistent Alignment Tool for DNA sequences

ACANA

:: DESCRIPTION

ACANA  (ACcurate ANchoring Alignment)) is an accurate and consistent alignment tool for DNA sequences. ACANA is specifically designed for aligning sequences that share only some moderately conserved regions and/or have a high frequency of long insertions or deletions. It attempts to combine the best of local and global alignments algorithms in searching for evolutionarily related regions of sequences in order to achieve the best alignment. ACANA is also robust to the small changes of alignment parameters, particularly the gap extension score. As an accurate alignment tool, ACANA is particularly useful in comparative sequence analysis for identifying conserved functional regulatory elements.

::DEVELOPER

ACANA team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux /MacOsX

:: DOWNLOAD

 ACANA

:: MORE INFORMATION

Citation

Weichun Huang, David M. Umbach, and Leping Li,
Accurate anchoring alignment of divergent sequences.
Bioinformatics 22:29-34, Jan 1 2006

DECIPHER 2.0.2 – Decipher & Manage DNA Sequences

DECIPHER 2.0.2

:: DESCRIPTION

DECIPHER (Database Enabled Code for Ideal Probe Hybridization Employing R) is a software toolset that can be used for deciphering and managing DNA sequences efficiently using the R statistical programming language.  The program is designed to be used with non-destructive workflows that guide the user through the process of importing, maintaining, analyzing, manipulating, and exporting a massive amount of DNA sequences.

::DEVELOPER

Erik Wright

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 DECIPHER

:: MORE INFORMATION

Citation

DesignSignatures: a tool for designing primers that yield amplicons with distinct signatures.
Wright ES, Vetsigian KH.
Bioinformatics. 2016 Jan 23. pii: btw047

ES Wright et al. (2011)
DECIPHER: A Search-Based Approach to Chimera Identification for 16S rRNA Sequences.”
Applied and Environmental Microbiology,

igrep – DNA Sequence Matching

igrep

:: DESCRIPTION

igrep is a fast CUDA implementation of agrep algorithm for approximate nucleotide sequence matching

::DEVELOPER

Hongjian Li

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Hongjian Li, Bing Ni, Man-Hon Wong, and Kwong-Sak Leung.
A Fast CUDA Implementation of Agrep Algorithm for Approximate Nucleotide Sequence Matching.
In Proceedings of the 9th IEEE Symposium on Application Specific Processors (SASP), pp.74-77, San Diego, United States, 5-6 June 2011. DOI: 10.1109/SASP.2011.5941082

DanQ – A Hybrid Convolutional and Recurrent Neural Network for predicting the function of DNA Sequences

DanQ

:: DESCRIPTION

DanQ is a hybrid convolutional and recurrent neural network model for predicting the function of DNA de novo from sequence.

::DEVELOPER

CBCL Lab (Computational Biology and Computational Learning) @ UCI

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 DanQ

:: MORE INFORMATION

Citation

DanQ: a hybrid convolutional and recurrent deep neural network for quantifying the function of DNA sequences.
Quang D, Xie X.
Nucleic Acids Res. 2016 Apr 15. pii: gkw226.