Crann 1.04 – Detect Adaptive Evolution in Protein-coding DNA Sequences

Crann 1.04

:: DESCRIPTION

Crann (pronounced ‘crown’) is the Irish word for ‘tree’.Crann has been developed in order to provide fast heuristic methods of detecting adaptive evolution in protein-coding genes. It is important that the user understands the advantages and limitations of these methods. It is also important for the user to know that the software is designed to perform a number of different tasks, however the interpretation of the results is left entirely to the user.

::DEVELOPER

McInerney lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOS

:: DOWNLOAD

Crann

:: MORE INFORMATION

Citation:

Creevey, C. and J. O. McInerney (2003).
CRANN: Detecting adaptive evolution in protein-coding DNA sequences
Bioinformatics (2003) 19: 1726.

RepeatMasker 4.1.0 – Screen DNA Sequences for Interspersed Repeats and Low Complexity DNA Sequences

RepeatMasker 4.1.0

:: DESCRIPTION

RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns). On average, almost 50% of a human genomic DNA sequence currently will be masked by the program. Sequence comparisons in RepeatMasker are performed by one of several popular search engines including, cross_match, ABBlast/WUBlast, RMBlast and Decypher.

::DEVELOPER

RepeatMasker Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 RepeatMasker

:: MORE INFORMATION

Citation

Genome Res. 2008 Aug;18(8):1362-8. Epub 2008 May 23.
DupMasker: a tool for annotating primate segmental duplications.
Jiang Z, Hubley R, Smit A, Eichler EE.

N-score – Predict Nucleosome Positions from DNA Sequence information

N-score

:: DESCRIPTION

N-score is a wavelet analysis based model for predicting nucleosome positions from DNA sequence information.

::DEVELOPER

Guo-CHeng Yuan Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • Python/Matlab

:: DOWNLOAD

 N-score

:: MORE INFORMATION

Citation

Genomic sequence is highly predictive of local nucleosome depletion.
Yuan GC, Liu JS.
PLoS Comput Biol. 2008 Jan;4(1):e13

TIGER – DNA Sequence Assembly

TIGER

:: DESCRIPTION

Tiger is a novel de novo assembly framework  which adapts to available computing resources by iteratively decomposing the assembly problem into sub-problems.

::DEVELOPER

IMPACT Reach Group (Illinois Microarchitecture Project using Algorithms and Compiler Technology)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
:: DOWNLOAD

 TIGER

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2012;13 Suppl 19:S18. doi: 10.1186/1471-2105-13-S19-S18. Epub 2012 Dec 19.
TIGER: tiled iterative genome assembler.
Wu XL1, Heo Y, El Hajj I, Hwu WM, Chen D, Ma J.

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.