DAMBE 5.3.48 – Sequence Data Analysis in Molecular Biology and Evolution

DAMBE 5.3.48

:: DESCRIPTION

DAMBE (data analysis in molecular biology and evolution) is an integrated software package for converting, manipulating, statistically and graphically describing, and analyzing molecular sequence data.

::DEVELOPER

Dr. Xuhua Xia

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / Mac OsX

:: DOWNLOAD

DAMBE

:: MORE INFORMATION

Citation:

Xia, X. 2013.
DAMBE5: A comprehensive software package for data analysis in molecular biology and evolution.
Molecular Biology and Evolution 30:1720-1728

Xia, X., and Xie. Z., 2001
DAMBE: Data analysis in molecular biology and evolution.
Journal of Heredity 92:371-373.

ChIA-PET 1.0 – Processing of ChIA-PET sequence data

ChIA-PET 1.0

:: DESCRIPTION

ChIA-PET Tool  is a software package for automatic processing of ChIA-PET (Chromatin Interaction Analysis using Paired-End Tag sequencing )sequence data, including linker filtering, mapping tags to reference genomes, identifying protein binding sites and chromatin interactions, and displaying the results on a graphical genome browser

:: DEVELOPER

the Genome Institute of Singapore

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Apach
  • MySQL
  • PHP
  • Java
  • R package
  • C Compiler

:: DOWNLOAD

 ChIA-PET 

:: MORE INFORMATION

Citation

ChIA-PET analysis of transcriptional chromatin interactions.
Zhang J, Poh HM, Peh SQ, Sia YY, Li G, Mulawadi FH, Goh Y, Fullwood MJ, Sung WK, Ruan X, Ruan Y.
Methods. 2012 Nov;58(3):289-99.

Sequence Scanner 1.0 – View, Edit, Print and Export sequence data

Sequence Scanner 1.0

:: DESCRIPTION

Sequence Scanner Software enables you to view, edit, print and export sequence data generated using the Applied Biosystems Genetic Analyzers. The software generates graphically expressive reports on results.

::DEVELOPER

Life Technologies

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

Sequence Scanner

:: MORE INFORMATION

3SEQ 1.1.0812 – Software for Detecting Recombination in Sequence data

3SEQ 1.1.0812

:: DESCRIPTION

3SEQ is a software program for identifying mosaic structure or recombination in nucleotide sequence data. 3SEQ takes as input a data set with a minimum of three aligned sequences, and it tests whether any sequence in the data set is a recombinant or mosaic of any other two sequences in the data set.

::DEVELOPER

the Mathematical Modeling and Bioinformatics Group at the Oxford University Clinical Research Unit (OUCRU)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • C++ Compiler

:: DOWNLOAD

  3SEQ 

:: MORE INFORMATION

Citation

Boni MF, Posada D, Feldman MW.
An exact nonparametric method for inferring mosaic structure in sequence triplets.
Genetics, 176:1035-1047, 2007.

VICUNA 1.1 – de novo Assembler for Ultra-deep Sequence data

VICUNA 1.1

:: DESCRIPTION

VICUNA is a de novo assembly program targeting populations with high mutation rates. It creates a single linear representation of the mixed population on which intra-host variants can be mapped. For clinical samples rich in contamination (e.g., >95%), VICUNA can leverage existing genomes, if available, to assemble only target-alike reads. After initial assembly, it can also use existing genomes to perform guided merging of contigs. For each data set (e.g., Illumina paired read, 454), VICUNA outputs consensus sequence(s) and the corresponding multiple sequence alignment of constituent reads.

::DEVELOPER

Computational R&D, The Broad Institute, Cambridge, MA

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 VICUNA

:: MORE INFORMATION

Citation

Xiao Yang, Patrick Charlebois, Sante Gnerre, Matthew G Coole, Niall J. Lennon, Joshua Z. Levin, James Qu, Elizabeth M. Ryan, Michael C. Zody, and Matthew R. Henn (2012)
De novo assembly of highly diverse viral populations.
BMC Genomics 13:475.