Main logo
?
tutorial arrow
×
Submit new tools
Share tools covering the current topic. Provide easy-to-follow guidelines to improve their usability.
Share new tools with the community
Sign up for free to promote the availability of bioinformatics tools

File format conversion bioinformatics software tools

G T A T C G C T A
SAMtools
Desktop

SAMtools

A suite of programs for interacting with high-throughput sequencing data. It…

A suite of programs for interacting with high-throughput sequencing data. It can manipulate alignments in the SAM/BAM/CRAM formats : reading, writing, editing, indexing, viewing and converting…

G T A T C G C T A
SBML
Format

SBML The Systems Biology Markup Language

Allows to represent models for systems biology. SBML is an interchange format…

Allows to represent models for systems biology. SBML is an interchange format which aims for description of systems where biological entities are involved in, and modified by, processes that occur…

G T A T C G C T A
pepXMLTab
Desktop

pepXMLTab

Converts the “spectrum query” section of a pepXML file to a data frame and…

Converts the “spectrum query” section of a pepXML file to a data frame and filters the peptide spectrum matches (PSMs) based on a user-specified PSM false discovery rate (FDR) threshold.…

G T A T C G C T A
PGDSpider
Desktop

PGDSpider

Aims to facilitate data exchange and file conversions between population…

Aims to facilitate data exchange and file conversions between population genetics programs. PGDSpider is able to read 27 different file formats and can export data into 29 other file formats. It can…

G T A T C G C T A
SBML2LaTeX
Web
Desktop

SBML2LaTeX

Facilitates the complicated and cumbersome model development process by…

Facilitates the complicated and cumbersome model development process by providing a simple method to translate such models to human-readable reports. SBML2LaTeX is a Java-based stand-alone program to…

G T A T C G C T A
EscherConverter
Web
Desktop

EscherConverter

Reads files created with the graphical network editor Escher and converts them…

Reads files created with the graphical network editor Escher and converts them to files in community standard formats. EscherConverter is written in Java, and it is available as a standalone…

G T A T C G C T A
nmrML2ISA
Desktop

nmrML2ISA

Generates an ISA-Tab structured investigation out of nmrML files. nmrML2ISA…

Generates an ISA-Tab structured investigation out of nmrML files. nmrML2ISA reduces the time needed to capture metadata substantially (capturing 90% of metadata on assay and sample levels), is much…

G T A T C G C T A
mzML2ISA
Desktop

mzML2ISA

Allows to convert metabolomic studies in .mzML and .imzML format to the open…

Allows to convert metabolomic studies in .mzML and .imzML format to the open ISA-Tab standard. mzML2ISA reduces the time needed to capture metadata substantially (capturing 90% of metadata on assay…

G T A T C G C T A
proBAMconvert
Desktop

proBAMconvert

Converts common peptide identification files (mzIdentML, pepXML, mzTAB) to the…

Converts common peptide identification files (mzIdentML, pepXML, mzTAB) to the proBAM or proBED format. proBAMconvert reads files using pyteomics or a self-build parser. The software automatically…

G T A T C G C T A
BioPAX2SBML
Web
Desktop

BioPAX2SBML

Converts BioPAX level 2 and level 3 files into SBML files including the…

Converts BioPAX level 2 and level 3 files into SBML files including the Qualitative Models extension. BioPAX2SBML includes pathways from BioCarta, Reactome, and from the National Cancer Institute,…

G T A T C G C T A
Risa
Desktop

Risa

Simplifies the integration of metadata in the experimental workflow and fills…

Simplifies the integration of metadata in the experimental workflow and fills the gap between the ISA-compliant data collection and curation and the data analysis phases. Risa provides generic…

G T A T C G C T A
nmrMLconvert
Web
Desktop

nmrMLconvert

Allows users to proceed file conversions from 1D nuclear magnetic resonance…

Allows users to proceed file conversions from 1D nuclear magnetic resonance spectroscopy (NMR) raw formats to nmrML. nmrMLconvert is a software available both as a web application and as a standalone…

G T A T C G C T A
SBMLPkgSpec
Desktop

SBMLPkgSpec

Furnishes a LaTeX document class corresponding to a standard document format…

Furnishes a LaTeX document class corresponding to a standard document format for SBML Level 3 package. SBMLPkgSpec contains a wide range of features such as: (i) define SBML package version and SBML…

G T A T C G C T A
NGS-FC
Desktop

NGS-FC Next-Generation Sequencing Format Converter

Allows users to support conversion between different Next Generation Sequencing…

Allows users to support conversion between different Next Generation Sequencing (NGS) files. NGS-FC is a crossed-platform software which summarizes information from 14 NGS databases. It can be used…

G T A T C G C T A
Pepxmltk
Desktop

Pepxmltk

Converts format for peptide identification results. Pepxmltk preserves…

Converts format for peptide identification results. Pepxmltk preserves information on total fragment ion intensity and can be used for peptide and protein quantitation. It also allows combining and…

G T A T C G C T A
(X)MedCon
Desktop

(X)MedCon

Resolves the complexities involved with conversion of medical image formats.…

Resolves the complexities involved with conversion of medical image formats. (X)MedCon is a framework divided into 4 modules : (i) xmedcon that provides a graphical user interface (GUI) to assist…

G T A T C G C T A
XSQ Tools
Desktop

XSQ Tools

Contains a set of utilities for XSQ file format conversions. The goal of the…

Contains a set of utilities for XSQ file format conversions. The goal of the XSQ Tools package is to lower the activation energy associated with adopting the XSQ format by providing documentation,…

G T A T C G C T A
GROK
Desktop

GROK Genomic Region Operation Toolkit

Facilitates translation of biomedical research questions to language amenable…

Facilitates translation of biomedical research questions to language amenable for computational analysis. GROK supports various deep sequencing (DS)-related operations such as preprocessing,…

G T A T C G C T A
Picard
Desktop

Picard

A set of tools (in Java) for working with next generation sequencing data in…

A set of tools (in Java) for working with next generation sequencing data in the BAM format.

G T A T C G C T A
fconv
Desktop

fconv

Intends to parse and manipulate multiple aspects and properties of molecular…

Intends to parse and manipulate multiple aspects and properties of molecular data. fconv is a robust and comprehensive tool involved in a broad range of computational workflows that are currently…

G T A T C G C T A
SraTailor
Desktop

SraTailor

A simple GUI software tool for visualizing published ChIP-seq raw data.…

A simple GUI software tool for visualizing published ChIP-seq raw data. SraTailor automatically converts an SRA into a BigWig-formatted file. Simplicity of use is one of the most notable features of…

G T A T C G C T A
nmrglue
Desktop

nmrglue

Allows users to handle multidimensional nuclear magnetic resonance (NMR) data.…

Allows users to handle multidimensional nuclear magnetic resonance (NMR) data. Nmrglue is a module whose main functions are reading, writing, and interacting with spectral data from multiple commons…

G T A T C G C T A
catfasta2phyml
Desktop

catfasta2phyml

Concatenates FASTA alignments to one file in different format. catfasta2phyml…

Concatenates FASTA alignments to one file in different format. catfasta2phyml is able to verify if all sequences in the file are aligned. It signals to users when an error is occurring.

G T A T C G C T A
GA2GEO
Web
Desktop

GA2GEO

Allows conversion of gene association files into an NCBI GEO format. GA2GEO is…

Allows conversion of gene association files into an NCBI GEO format. GA2GEO is able to import all gene ontology (GO) annotations for a gene product.

G T A T C G C T A
GOanna2ga
Web

GOanna2ga

Allows conversion of files returned by Goanna into a gene association file.…

Allows conversion of files returned by Goanna into a gene association file. Goanna2ga permits users to add data obtained from GOanna to the GORetriever annotations.

G T A T C G C T A
mgfToBinStack
Desktop

mgfToBinStack

Imports spectral data generated by Mascot. mgfToBinStack is an open source…

Imports spectral data generated by Mascot. mgfToBinStack is an open source software, part of QuiXoT Software, which can be used in association with MascotToQuiXML to convert files from MGF to binary…

G T A T C G C T A
MascotToQuiXML
Desktop

MascotToQuiXML

Allows users to convert Mascot data into QuiXML format. MascotToQuiXML can be…

Allows users to convert Mascot data into QuiXML format. MascotToQuiXML can be associated to mgfToBinStack to import data which has to be analyzed with QuiXoT. This software is part of the QuiXoT…

G T A T C G C T A
CSVToQuiXML
Desktop

CSVToQuiXML

Allows users to convert tab-separated text files. CSVToQuiXML is an open source…

Allows users to convert tab-separated text files. CSVToQuiXML is an open source software for switching files from CSV format to QuiXML with the aim of making them utilizable by QuiXoT.

G T A T C G C T A
RAWToBinStack
Desktop

RAWToBinStack

Converts spectral data from Thermo RAW files. RAWtoBinStack intends to…

Converts spectral data from Thermo RAW files. RAWtoBinStack intends to transform information to make them exploitable by QuiXoT. This software is part of QuiXoT Software Package.

G T A T C G C T A
SBML-Shorthand
Nontypeable

SBML-Shorthand

Allows building essential model structure. SBML-shorthand is a language for…

Allows building essential model structure. SBML-shorthand is a language for describing systems biology models.

G T A T C G C T A
sbmltidy
Desktop

sbmltidy

Reformats an SBML file. Sbmltidy invokes the program tidy to reformat an XML…

Reformats an SBML file. Sbmltidy invokes the program tidy to reformat an XML SBML file. This wrapper simplifies the task of invoking tidy on SBML files by supplying some preselected arguments.

G T A T C G C T A
SBML2XPP
Desktop

SBML2XPP

Converts SBML into XPPAut or Oscill8. SBML2XPP is a part of SBFC toolkit. This…

Converts SBML into XPPAut or Oscill8. SBML2XPP is a part of SBFC toolkit. This converter is based on JSBML, to support all the levels and versions of SBML until SBML level 3 version 1 core.

G T A T C G C T A
SBML2Octave
Desktop

SBML2Octave

Converts any SBML files into Octave. SBML2Octave is a part of SBFC toolkit.…

Converts any SBML files into Octave. SBML2Octave is a part of SBFC toolkit. This converter is based on JSBML, to support all the levels and versions of SBML until SBML level 3 version 1 core.

G T A T C G C T A
SBFC
Web
Desktop

SBFC Systems Biology Format Converter

Aims to translate any systems biology model format into another. The Systems…

Aims to translate any systems biology model format into another. The Systems Biology Format Converter (SBFC) is a Java generic framework that allows users to easily add new converters and to…

G T A T C G C T A
MathSBML
Desktop

MathSBML

Supports biological community and SBML users in particular. MathSBML is an…

Supports biological community and SBML users in particular. MathSBML is an open-source package for working with SBML models in Mathematica. It provides facilities for reading SBML models, converting…

G T A T C G C T A
SbmlViewer
Desktop

SbmlViewer

Allows users to read biological models written in SBML format. SbmlViewer is a…

Allows users to read biological models written in SBML format. SbmlViewer is a software that transforms SBML files into human readable formats.

MRIConvert…
Desktop

MRIConvert files

Permits users to convert one or multiple DICOM files. MRIConvert files allows…

Permits users to convert one or multiple DICOM files. MRIConvert files allows users to six other extensions: FSL NifTi, SPM Analyze, Meta Image, NifTi, Analyze 7.5 and BrainVoyager.

G T A T C G C T A
Pdb2mgif
Web

Pdb2mgif PDB to MultiGIF

Generates animated images of a molecular representation. Pdb2mgif creates…

Generates animated images of a molecular representation. Pdb2mgif creates animated images of molecules to be displayed by all standard web browsers without depending on an extra visualisation program.

G T A T C G C T A
ChIP2LAMP
Desktop

ChIP2LAMP

Allows conversion of ChIP-seq and RNA-seq results to input files for the…

Allows conversion of ChIP-seq and RNA-seq results to input files for the software LAMP (Limitless-Arity Multiple-testing Procedure).

seg-suite
Desktop

seg-suite

Contains a toolkit for arranging segments, alignments, and annotations of…

Contains a toolkit for arranging segments, alignments, and annotations of sequences. seg-suite performs composing alignments and is composed of a conversion program which transforms various formats…

G T A T C G C T A
Blast2Fasta
Web

Blast2Fasta

Allows conversion of the BLAST outputs from the NCBI into FASTA format.

Allows conversion of the BLAST outputs from the NCBI into FASTA format.

G T A T C G C T A
dcm2niix
Desktop

dcm2niix

Permits to convert proprietary Philips PAR/REC images to neuroimaging…

Permits to convert proprietary Philips PAR/REC images to neuroimaging informatics technology initiative (NIfTI). dcm2niix is easy to use, offers features to specify output file names. It is suitable…

G T A T C G C T A
Trapper
Desktop

Trapper

Converts Agilent MassHunter format (.d directories) to mzXML. Trapper is a…

Converts Agilent MassHunter format (.d directories) to mzXML. Trapper is a package for Windows that relies on the MassHunter Data Accquisition Component (MHDAC), which is included with the trapper…

G T A T C G C T A
mzWiff
Desktop

mzWiff

Converts analyst native acquisition (.wiff) files to mzXML. mzWiff is a package…

Converts analyst native acquisition (.wiff) files to mzXML. mzWiff is a package for Windows. This program is no longer supported.

G T A T C G C T A
massWolf
Desktop

massWolf

Converts MassLynx native acquisition files to mzXML. massWolf is a Visual C++…

Converts MassLynx native acquisition files to mzXML. massWolf is a Visual C++ package for Windows. This program is no longer supported.

G T A T C G C T A
ReAdW
Desktop

ReAdW

Converts Xcalibur native acquisition (.RAW) files to mzXML. ReAdW is a package…

Converts Xcalibur native acquisition (.RAW) files to mzXML. ReAdW is a package for Windows. This program is no longer supported.

G T A T C G C T A
bam2wig
Desktop

bam2wig

Converts a BAM alignment to wiggle and bigwig coverage files, with flexible…

Converts a BAM alignment to wiggle and bigwig coverage files, with flexible reporting options.

G T A T C G C T A
HarvestTools
Desktop

HarvestTools

Allows users to create an interface with Gingr files. HarvestTools can be used…

Allows users to create an interface with Gingr files. HarvestTools can be used to make generic conversion between standard bioinformatics file formats. It is a complement to the Harvest Suite that is…

G T A T C G C T A
Reformat
Desktop

Reformat

Converts sequence files between different formats such as fastq and fasta.…

Converts sequence files between different formats such as fastq and fasta. Reformat is designed for generic streaming read-processing tasks that have low memory or computational demands, such as…

G T A T C G C T A
ConverThor
Desktop

ConverThor

Performs format conversion between MODICOS and NTS formats. ConverThor is a…

Performs format conversion between MODICOS and NTS formats. ConverThor is a Java program.

G T A T C G C T A
AFLP converter
Desktop

AFLP converter

Performs a format conversion from AFLP-SURV program to DFDIST program. With the…

Performs a format conversion from AFLP-SURV program to DFDIST program. With the AFLP converter, user can decide to convert a complete file or choose any number of populations and/or loci. Missing…

G T A T C G C T A
chainToPslBasic
Desktop

chainToPslBasic

Converts files in CHAIN into PSLBASIC.

Converts files in CHAIN into PSLBASIC.

G T A T C G C T A
faToFastq
Desktop

faToFastq

Converts files in FA into FASTQ.

Converts files in FA into FASTQ.

G T A T C G C T A
faToTab
Desktop

faToTab

Converts files in FA into TAB.

Converts files in FA into TAB.

G T A T C G C T A
faToTwoBit
Desktop

faToTwoBit

Converts files in FA into TWOBIT.

Converts files in FA into TWOBIT.

G T A T C G C T A
fastqToFa
Desktop

fastqToFa

Converts files in FASTQ into FA.

Converts files in FASTQ into FA.

G T A T C G C T A
chainToPsl
Desktop

chainToPsl

Converts files in CHAIN into PSL.

Converts files in CHAIN into PSL.

G T A T C G C T A
chainToAxt
Desktop

chainToAxt

Converts files in CHAIN into AXT.

Converts files in CHAIN into AXT.

G T A T C G C T A
blastXmlToPsl
Desktop

blastXmlToPsl

Converts files in BLASTXML into PSL.

Converts files in BLASTXML into PSL.

G T A T C G C T A
blastToPsl
Desktop

blastToPsl

Converts files in BLAST into PSL.

Converts files in BLAST into PSL.

G T A T C G C T A
bigWigToWig
Desktop

bigWigToWig

Converts files in BIGWIG into WIG.

Converts files in BIGWIG into WIG.

G T A T C G C T A
bigWigToBedGrap…
Desktop

bigWigToBedGraph

Converts files in BIGWIG into BEDGRAPH.

Converts files in BIGWIG into BEDGRAPH.

G T A T C G C T A
bigPslToPsl
Desktop

bigPslToPsl

Converts files in BIGPSL into PSL.

Converts files in BIGPSL into PSL.

G T A T C G C T A
bigMafToMaf
Desktop

bigMafToMaf

Converts files in BIGMAF into MAF.

Converts files in BIGMAF into MAF.

G T A T C G C T A
bigBedToBed
Desktop

bigBedToBed

Converts files in BIGBED into BED.

Converts files in BIGBED into BED.

G T A T C G C T A
bedToPsl
Desktop

bedToPsl

Converts files in BED into PSL.

Converts files in BED into PSL.

G T A T C G C T A
bedToGenePred
Desktop

bedToGenePred

Converts files in BED into GENEPRED.

Converts files in BED into GENEPRED.

G T A T C G C T A
bedtoBigBed
Desktop

bedtoBigBed

Converts files in BED into BIGBED.

Converts files in BED into BIGBED.

G T A T C G C T A
bamToPsl
Desktop

bamToPsl

Converts files in BAM into PSL.

Converts files in BAM into PSL.

G T A T C G C T A
axtToPsl
Desktop

axtToPsl

Converts files in AXT into PSL.

Converts files in AXT into PSL.

G T A T C G C T A
axtToMaf
Desktop

axtToMaf

Converts files in AXT into MAF.

Converts files in AXT into MAF.

G T A T C G C T A
wigToBigWig
Desktop

wigToBigWig

Permits to converts WIG file into BIGWIG file.

Permits to converts WIG file into BIGWIG file.

G T A T C G C T A
pslxToFa
Desktop

pslxToFa

Permits to converts PSLX file into FA file.

Permits to converts PSLX file into FA file.

G T A T C G C T A
pslToPslx
Desktop

pslToPslx

Permits to converts PSL file into PSLX file.

Permits to converts PSL file into PSLX file.

G T A T C G C T A
pslToChain
Desktop

pslToChain

Permits to converts PSL file into CHAIN file.

Permits to converts PSL file into CHAIN file.

G T A T C G C T A
pslToBigPsl
Desktop

pslToBigPsl

Permits to converts PSL file into BIGPSL file.

Permits to converts PSL file into BIGPSL file.

G T A T C G C T A
pslToBed
Desktop

pslToBed

Permits to converts PSL file into BED file.

Permits to converts PSL file into BED file.

G T A T C G C T A
mafToSnpBed
Desktop

mafToSnpBed

Permits to converts MAF file into SNPBED file.

Permits to converts MAF file into SNPBED file.

G T A T C G C T A
netToBed
Desktop

netToBed

Permits to converts NET file into BED file.

Permits to converts NET file into BED file.

G T A T C G C T A
netToAxt
Desktop

netToAxt

Permits to converts NET file into AXT file.

Permits to converts NET file into AXT file.

G T A T C G C T A
mafToPsl
Desktop

mafToPsl

Permits to converts MAF file into PSL file.

Permits to converts MAF file into PSL file.

G T A T C G C T A
mafToBigMaf
Desktop

mafToBigMaf

Permits to converts MAF file into BIGMAF file.

Permits to converts MAF file into BIGMAF file.

G T A T C G C T A
mafToAxt
Desktop

mafToAxt

Permits to converts MAF file into AXT file.

Permits to converts MAF file into AXT file.

G T A T C G C T A
lavToPsl
Desktop

lavToPsl

Permits to converts LAV file into PSL file.

Permits to converts LAV file into PSL file.

G T A T C G C T A
lavToAxt
Desktop

lavToAxt

Permits to converts LAV file into AXT file.

Permits to converts LAV file into AXT file.

G T A T C G C T A
gtfToGenePred
Desktop

gtfToGenePred

Permits to converts GTF file into GENEPRED file.

Permits to converts GTF file into GENEPRED file.

G T A T C G C T A
gff3ToPsl
Desktop

gff3ToPsl

Permits to converts GFF3 file into PSL file.

Permits to converts GFF3 file into PSL file.

G T A T C G C T A
gff3ToGenePred
Desktop

gff3ToGenePred

Permits to converts GFF3 file into GENEPRED file.

Permits to converts GFF3 file into GENEPRED file.

G T A T C G C T A
genePredToGtf
Desktop

genePredToGtf

Permits to converts GENEPRED file into GTF file.

Permits to converts GENEPRED file into GTF file.

G T A T C G C T A
genePredToFakeP…
Desktop

genePredToFakePsl

Permits to converts GENEPRED file into FAKEPSL file.

Permits to converts GENEPRED file into FAKEPSL file.

G T A T C G C T A
genePredToBigGe…
Desktop

genePredToBigGenePred

Permits to converts GENEPRED file into BIGGENEPRED file.

Permits to converts GENEPRED file into BIGGENEPRED file.

G T A T C G C T A
genePredToBed
Desktop

genePredToBed

Permits to converts GENEPRED file into BED file.

Permits to converts GENEPRED file into BED file.

G T A T C G C T A
Uncle PSL
Desktop

Uncle PSL

Performs conversion of BLAT output (PSL format) to SAM format. Uncle PSL offers…

Performs conversion of BLAT output (PSL format) to SAM format. Uncle PSL offers conversion that was tested on simulated reads against output generated by bwa mem. The logic is based on the psl2sam.pl…

G T A T C G C T A
pbh5tools
Desktop

pbh5tools

Tools for manipulating HDF5 files produced by Pacific Biosciences.…

Tools for manipulating HDF5 files produced by Pacific Biosciences. Specifically, this package provides functionality for manipulating and extracting data from "cmp.h5" and…

G T A T C G C T A
pbcore
Desktop

pbcore

A Python library for reading and writing PacBio data files.

A Python library for reading and writing PacBio data files.

G T A T C G C T A
srf2fastq
Desktop

srf2fastq

A convert for SFR files into Sanger fastq format. srf2fastq extracts sequences…

A convert for SFR files into Sanger fastq format. srf2fastq extracts sequences and qualities from one or more SRF archives and writes them in Sanger fastq format to stdout.

G T A T C G C T A
NCBI SRA…
Desktop

NCBI SRA Toolkit

Enables reading of sequencing files from the SRA database and writing files…

Enables reading of sequencing files from the SRA database and writing files into the same format. The NCBI SRA Toolkit is provided in the form of the SRA SDK, and can be compiled with GCC. It allows…

G T A T C G C T A
FASTX-Toolkit
Desktop

FASTX-Toolkit

A collection of command line tools for Short-Reads FASTA/FASTQ files…

A collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing. Next-Generation sequencing machines usually produce FASTA or FASTQ files, containing multiple short-reads sequences…

Information

By using OMICtools you acknowledge that you have read and accepted the terms of the end user license agreement.