Tag: Conversion

CREATE 1.37 – Creation of new and Conversion of Existing data input files for 64 Genetic software

CREATE 1.37

:: DESCRIPTION

CREATE is software for the creation of new and conversion of existing data input files for 64 genetic data analysis software programs. Programs are grouped into areas of sibship reconstruction, parentage assignment, effective population size, quantitative genetics, general genetic data analysis, and specialized genetic applications.

::DEVELOPER

Jason Coombs ,jcoombs@cns.umass.edu ,Ben Letcher, and Keith Nislow

:: SCREENSHOTS

CREATE

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 CREATE

:: MORE INFORMATION

Citation

create: a software to create input files from diploid genotypic data for 52 genetic software programs.
Coombs JA, Letcher BH, Nislow KH.
Mol Ecol Resour. 2008 May;8(3):578-80. doi: 10.1111/j.1471-8286.2007.02036.x.

SNP tools 1.80 – Analysis and Conversion of Genotype data

SNP tools 1.80

:: DESCRIPTION

SNP tools is a general add-in for Microsoft Excel to do data conversion and basic analysis for Single Nucleotide Polymorphism (SNP) data.

::DEVELOPER

Dr. Bowang Chen

:: SCREENSHOTS

SNPtools

:: REQUIREMENTS

  • Windows/ MacOsX
  • Excel

:: DOWNLOAD

  SNP tools

:: MORE INFORMATION

Citation

Chen, B., et al.,
SNP_tools: A compact tool package for analysis and conversion of genotype data for MS-Excel.
BMC Res Notes, 2009. 2(1): p. 214.

ForCon 1.0 – Conversion of Nucleic Acid & Amino Acid Sequence Alignments

ForCon 1.0

:: DESCRIPTION

ForCon is a user-friendly software tool for the conversion of nucleic acid and amino acid sequence alignments. Many software packages for sequence alignment and the construction of evolutionary trees have implemented their own standard of saving and reading sequence alignments. To circumvent the labourious work of manually converting alignment formats with the use of a word processor, this program was written: it converts these formats automatically.

::DEVELOPER

Jeroen Raes

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

ForCon

:: MORE INFORMATION

Citation

Raes, J. and Van de Peer,Y. (1999)
ForCon : a software tool for the conversion of sequence alignments.
EMBnet.news 6(1).

FASTA BLAST Scan 2.4 – FASTA & BLAST Alignment Conversion

FASTA BLAST Scan 2.4

:: DESCRIPTION

FASTA BLAST Scan is a program for processing nucleotide sequences alignment made with FASTA and BLAST alignment tools.

::DEVELOPER

Olivier Friard

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

FASTA BLAST Scan

:: MORE INFORMATION

FASTA BLAST Scan is released under the GNU General Public License (GPL)

Mol2Mol 5.6.3 – Molecule File Manipulation & Conversion

Mol2Mol 5.6.3

:: DESCRIPTION

Mol2Mol is a menu-driven program that converts between the file formats used by the major PC modeling programs.

Mol2Mol recognizes, reads and writes about 50 different file formats and subformats. It contains a simple graphic display module to inspect the currently loaded molecule. It possesses some chemical intelligence for recognizing detailed atom types, hybridization and chemical environments, which is necessary for converting simpler formats (like X-ray crystallographic files) to more advanced ones, or when hydrogen atoms are automatically to be added to the heavy atoms. Problematic files can be corrected within Mol2mol or as ASCII files by calling directly your favourite text editor.

Mol2Mol can convert molecular files into POV-Ray files. As with POV-Ray in general, you can create not only serious scientific illustrations, but surrealistic or funny images as well.

::DEVELOPER

Dr. Tamas E. Gunda

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

Mol2Mol trial version

:: MORE INFORMATION

Mol2Mol is a shareware. Mol2Mol single user licence: € 39.  Buy Mol2Mol now via Share-It! with your credit card.

med2bib 1.04 / toc2bib 1.04 – MEDLINE and TOC/DOC to BibTeX Conversion

med2bib 1.04 / toc2bib 1.04

:: DESCRIPTION

med2bib converts MEDLINE full-record ASCII bibliographic entries for journal articles into BibTeX entries.

toc2bib converts TOC/DOC (the electronic literature search engine available at Caltech) full-record entries.

::DEVELOPER

Laurent Itti, itti@klab.caltech.edu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 med2bib / toc2bib

:: MORE INFORMATION

PAL2NAL v14 – Conversion of Protein Sequence Alignments into Corresponding Codon Alignments

PAL2NAL v14

:: DESCRIPTION

PAL2NAL is a program that converts a multiple sequence alignment of proteins and the corresponding DNA (or mRNA) sequences into a codon alignment. The program automatically assigns the corresponding codon sequence even if the input DNA sequence has mismatches with the input protein sequence, or contains UTRs, polyA tails. It can also deal with frame shifts in the input alignment, which is suitable for the analysis of pseudogenes. The resulting codon alignment can further be subjected to the calculation of synonymous (dS) and non-synonymous (dN) substitution rates.

::DEVELOPER

Mikita Suyama 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 PAL2NAL

:: MORE INFORMATION

Citation

Mikita Suyama, David Torrents, and Peer Bork (2006)
PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments.
Nucleic Acids Res. 34, W609-W612.

Translate.wdgt – DNA/Protein Conversions

Translate.wdgt

:: DESCRIPTION

Translate.wdgt is for DNA/Protein conversions.

Manipulates DNA or protein sequences.

  • Translate DNA to protein, 3 frames
  • Reverse translate protein to DNA, using human-optimized codons
  • Format (60 characters per line in groups of 10, numbered at line breaks)
  • Scramble
  • Make antiparallel (complementary) strand

::DEVELOPER

Ian York

:: SCREENSHOTS

:: REQUIREMENTS

  • MacOS 10.4 or higher

:: DOWNLOAD

Translate.wdgt

:: MORE INFORMATION

N/A

SBML Converters 20100413 – Conversions to & from SBML

SBML Converters 20100413

:: DESCRIPTION

SBML Converters are several converters which transfer SBML to BioPax 2 and 3, SBML to XPP and SBML to Octave, etc.

Converters list:

  • SBML to Octave  (GNU Octave is a high-level language, primarily intended for numerical computations. It provides a convenient command line interface for solving linear and nonlinear problems numerically, and for performing other numerical experiments using a language that is mostly compatible with Matlab.)
  • SBML to XPP (XPP-Aut is a numerical analysis software. It permits to solve differential equations, difference equations, delay equations, functional equations, boundary value problems, and stochastic equations.)
  • SBML to SciLab (SciLab is a scientific software package for numerical computations providing a powerful open computing environment for engineering and scientific applications.)
  • SBML to CellML & CellML to SBML (CellML is an open standard based on the XML markup language like SBML. CellML is being developed by the Bioengineering Institute at the University of Auckland and affiliated research groups. The main difference between CellML and SBML is that the former is based on modules while the latter is based on hierarchical components.)
  • SBML to BioPax (The main objective of the BioPAX initiative is to develop a data exchange format for biological pathways that is flexible, extensible, optionally encapsulated and compatible with other standards and can be widely adopted in a timely manner.)
  • SBML to Dot (GraphViz is an open source graph visualization software. The language used to encode the graphics processed by GraphViz is called DOT. Note that a “dot” file can be used with other graphical software.)
  • SBML to SVG (Scalable Vector Graphics (SVG) is a language for describing two-dimensional graphics and graphical applications in XML. It is an open standard created by the World Wide Web Consortium.)

SBML Converters also have an online version.

::DEVELOPER

Computational Systems Neurobiology Group, EBI

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

SBML Converters

:: MORE INFORMATION

Please send any help requests or bug reports to : biomodels-net-support at lists.sourceforge.net