OrthoXML 0.3 / SeqXML 0.4 – XML standards for Orthology and Sequence Information

OrthoXML 0.3 / SeqXML 0.4

:: DESCRIPTION

OrthoXML is designed broadly to allow the storage and comparison of orthology data from any ortholog database. It establishes a structure for describing orthology relationships while still allowing flexibility for database-specific information to be encapsulated in the same format.

The SeqXML schema (XSD) defines the skeletal structure of the sequence files and allows one to set constraints for each type of data it contains: for example, one can limit a DNA sequence to consist only of {A,G,C,T,N}. If one then tries to import a DNA sequence containing a ‘Z’, this error will be detected automatically by any XML validator.

:: DEVELOPER

Sonnhammer Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

OrthoXML  / SeqXML

:: MORE INFORMATION

Split fasta – Split large FASTA file into smaller files

Split fasta

:: DESCRIPTION

Split fasta file into smaller segments. This is useful if you have a large FASTA file that needs to be split into smaller files.

::DEVELOPER

CABM Structural Bioinformatics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Perl

:: DOWNLOAD

  Split fasta

:: MORE INFORMATION

genio 1.0.12 – Genetics Input/Output Functions

genio 1.0.12

:: DESCRIPTION

The genio (GENetics I/O) package provides easy-to-use and efficient readers and writers for formats in genetics research.

::DEVELOPER

The Ochoa Lab 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX / Windows
  • R

:: DOWNLOAD

genio

:: MORE INFORMATION

Gro2mat – A package to efficiently read Gromacs output in Matlab

Gro2mat

:: DESCRIPTION

gro2mat is a package that allows fast and easy access to Gromacs output files from Matlab.

::DEVELOPER

Oxford Protein Informatics Group (OPIG)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • MatLab

:: DOWNLOAD

 Gro2mat

:: MORE INFORMATION

Citation

J Comput Chem. 2014 Jul 30;35(20):1528-31. doi: 10.1002/jcc.23650. Epub 2014 Jun 12.
Gro2mat: a package to efficiently read gromacs output in MATLAB.
Dien H1, Deane CM, Knapp B.

HapZipper – Compression Scheme for HapMap Phase III Phased Data

HapZipper

:: DESCRIPTION

HapZipper is a lossless compression tool tailored to compress HapMap data beyond benchmarks defined by generic tools such as gzip, bzip2 and lzma.

::DEVELOPER

Joel Bader lab

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux / Windows
  • JRE

:: DOWNLOAD

 HapZipper

:: MORE INFORMATION

Citation

HapZipper: sharing HapMap populations just got easier.
Chanda P, Elhaik E, Bader JS.
Nucleic Acids Res. 2012 Nov 1;40(20):e159. doi: 10.1093/nar/gks709.

Cassandra v15.4.10 – Combines Annovar Output with other Public Datasources to Output Annotated .vcf Files.

Cassandra v15.4.10

:: DESCRIPTION

Cassandra combines annovar output with other public datasources to output annotated .vcf files.

::DEVELOPER

Human Genome Sequencing Center, Baylor College of Medicine

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  MacOsX
  • Java
  • Perl
  • Annovar

:: DOWNLOAD

Cassandra

:: MORE INFORMATION

ReadTools 1.5.2 – Universal Toolkit for Handling Sequence data from different Sequencing Platforms

ReadTools 1.5.2

:: DESCRIPTION

ReadTools provides a consistent and highly tested set of tools for processing sequencing data from any kind of source and focusing on raw reads, while including tools for mapped reads as well.

DEVELOPER

Institute of Population Genetics, University of Veterinary Medicine Vienna

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Java

:: DOWNLOAD

ReadTools

:: MORE INFORMATION

Citation:

Mol Ecol Resour. 2018 May;18(3):676-680. doi: 10.1111/1755-0998.12741. Epub 2017 Dec 8.
ReadTools: A universal toolkit for handling sequence data from different sequencing platforms.
Gómez-Sánchez D,SchlöttererÇ

ms2ms.pl – Convert the Output of Hudson’s Makesample software into Microsatellite data

ms2ms.pl

:: DESCRIPTION

ms2ms.pl converts the output of Hudson’s makesample software into microsatellite data. The output could be directly analyzed by MSA.

DEVELOPER

Institute of Population Genetics, University of Veterinary Medicine Vienna

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Perl

:: DOWNLOAD

 ms2ms.pl

:: MORE INFORMATION

Citation

SREENIVASA R. PIDUGU andCHRISTIAN SCHLÖTTERER
ms2ms.pl: a PERL script for generating microsatellite data
Molecular Ecology Notes Volume 6, Issue 2, pages 580–581, June 2006

MINCE v0.5.0 ‐ Bucketing-based Reference-free Compression

MINCE v0.5.0

:: DESCRIPTION

MINCE is a technique for encoding collections of short reads so that they can be more effectively compressed via a standard compressor like LZIP.

::DEVELOPER

Kingsford Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOs

:: DOWNLOAD

MINCE

:: MORE INFORMATION

Citation

Bioinformatics. 2015 Sep 1;31(17):2770-7. doi: 10.1093/bioinformatics/btv248. Epub 2015 Apr 24.
Data-dependent bucketing improves reference-free compression of sequencing reads.
Patro R, Kingsford C.

Referee – Rapid, Separable Compression for Sequence Alignments

Referee

:: DESCRIPTION

Referee is a command-line tool that takes sequence alignment SAM files and compresses them in a lossless manner.

::DEVELOPER

Kingsford Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOs

:: DOWNLOAD

Referee

:: MORE INFORMATION

Citation

Darya Filippova, Carl Kingsford (2015).
Rapid, separable compression enables fast analyses of sequence alignments.
Proceedings of the 6th ACM Conference on Bioinformatics, Computational Biology and Health Informatics, pages 194-201.