File Conversion
- PRIDE Converter 2.0.17 – Converts Mass Spectrometry Data into PRIDE XML
- Janus – Convert CSV and Tab-delimited files to Nexus data files
- FASTA Canonical Sequences 1.1 – Delete Comments from FASTA file
- ExSer 1.0 – Mine Protein Data Bank (PDB) for Secondary Structural Elements
- SeqMaT – Sequence Manipulation Tool for Phylogenetic Analysis
- NGC 0.0.1 – Compressor for High-throughput Sequencing data
- DELIMINATE – Method for Loss-less Compression of Genomic Sequences
- SPLITLOC 1.0 – Split Locus Files
- BiSSAP 1.2 – Biological Sequence Submission Application for Patents
- Checker 4.4.6 – Checking Biotechnology Sequence Listings for Compliance with Format
- PatentIn 3.5.1 – Preparing Sequence Listings for Patent Application
- Uniprot DAT File Parser 1.1.4511 – Read Uniprot (IPI) .Dat file and Parse out the information for each entry
- BioData-SF 1.0 – Bioinformatics Data Standardization Formatter
- seqmagick 0.5.0 – Convert Sequence Files between Formats
- fastareader 0.1 – Read FASTA files in a Text or Binary Format
- SAM2Pretty 1.1 – Convert a SAM entry to a human readable and more Verbose Format
- DSRC 1.02 — DNA Sequence Reads Compression
- Pysam 0.7.4 – Python module for Reading and Manipulating Sam files
- BIOM-FORMAT 1.1.2 – The Biological Observation Matrix format
- MADGene 2.1 / eMADGene 1.0 – Translate between Disparate Gene Identifiers for the Same Gene
- P2S 29 – Converting files from Plink to Sumstat format
- Giflu – Generate Input files suitable for Baesc from Luminex system output
- NAOMI – Conversion of Common Chemical File Formats
- PGDSpider 2.0.3.0 – Data conversion tool for Population Genetic and Genomics Programs
- SBML2LATEX 0.9.9 – Conversion of SBML files into Human-readable Reports
- KEGGtranslator 2.3.0 – Visualizing and Converting the KEGG PATHWAY database to various formats
- BioPAX2SBML – Translation of BioPAX into SBML including the Qualitative Models extension
- BioImage Convert 1.53 – Image Conversion Utility
- bam2fastq 1.1.0 – Extract Sequences from a BAM file in Fastq format
- VCFtools 0.1.10 – Program Package designed for working with VCF files
- sff_extract 0.3.0 – Extract the reads from the sff files into Fasta / xml/ caf file
- mtDNASeqSampling 20050928 – Sample mtDNA Sequences from a certain dataset to Test Sampling Issues
- mtDNASeqback 20050407 – Recover mtDNA Sequence data from Haplotype data
- STR-FST 20050915 – Obtain FST Matrix from STR Allele Frequency data
- EmblEx 20121203 – Parse and Extract data from EMBL entries to various formats
- XML2RAF 1.01 -Create RAF Maps from PDB XML files
- Open Babel 2.3.2 – Converter for Chemistry & Molecular Modeling Data Files
- RLZ 0.1.1 – Relative Lempel-Ziv Compression of Genomes for Large-Scale Storage and Retrieval
- FragSort 1.0.0 – Fragment Sort
- RmscopII 2.2 – Redirect PDB files or RasMol scripts to multiple RasMol sessions
- TableParser – Extract Sequences from Tab-delimited Assembly Alignment Files
- AceParser 1.33 – Parse an Ace file (Phred/Phrap output) into a tab-delimited Assembly Alignment file
- FastaFormat / FastQFormat / UnFastaFormat / UnFastQFormat – Conversion between Tab-delimited files and FASTA/ FastQ Format
- PDB Validation Suite 8.061 – tools for Processing and Checking Structure data
- MMCIF Dictionary Suite 2.200 – Parse, Validate, Manage data dictionaries used by the PDB
- sf-convert 1.200 – Converting Structure Factors from one Format to Another
- MAXIT 8.120 – An application for Processing and Annotating of Macromolecular Structure data
- CIFTr 2.053 – Translate mmCIF data files into PDB format
- PDBML2CIF 2.011 – Convert PDBML data files into mmCIF data files
- Power Graph Analysis Tool 20080823 – Convert Graphs into Power Graphs
- VCF2GEN 1.1 – Convert VCF format to GEN format
- Scriptome – Protocols for Manipulating Biological Data
- PyMsXML 0.5.4 – Convert Vendor Specific Mass Spectrometry file formats to open XML file formats
- Phoenix 1.0 – Parser for EMBL-Bank Flat files
- iConvert.pl – Convert Tree Files and Sequence Files between common Formats
- SCALCE 2.3 – FASTQ Compression tool
- PklFileMerger – Conversion of single Q-TOF pkl-files into larger Mergefiles
- CELUTIL 1.0 – Convert Cel format into XDA / ASCII format
- blast2malign 0.3 – Create Multiple Alignment from the database hits of a BLAST search
- Bio-Formats 4.4.4 – Java Library for Reading & Writing Biology Image File Formats
- track 1.1.0 – Read/Write Access to Genomic Tracks
- SBMLToolbox 4.1.0 – SBML models toolbox for MATLAB users
- PDBQT Converter 20110806 – Convert .mol2 and .pdb Files to .pdbqt Format
- bioscripts.convert 0.4 – Biopython Scripts for Converting Molecular Sequences
- GeneStudio™ Pro 2.2.0.0 – Sequence Format Conversion Engine and More
- SeqVerter 2.0.4.4 – Sequence File Format Conversion Utility
- ForCon 1.0 – Conversion of Nucleic Acid & Amino Acid Sequence Alignments
- STR_ConvertFormats 20120306 – Transform STR typing data to Genotyper table format
- FASTA BLAST Scan 2.4 – FASTA & BLAST Alignment Conversion
- SimPheny to SBML l2v1 – Convert SimPheny output to SBML
- SFF Workbench 1.5 – Simple SFF File Editor & Converter
- asm2ace 0.6 – Convert the Celera ASM format to ACE or CAF file format
- PDB2PQR 1.8 – Convert Protein files in PDB format to PQR format
- fasta2pfam.pl – Convert Fasta file to Pfam format
- ms2ms.pl – Convert the Output of Hudson’s Makesample software into Microsatellite data
- clean_reads 0.2.3 – Clean NGS reads
- Mol2Mol 5.6.3 – Molecule File Manipulation & Conversion
- MolPOV 2.1.0 – PDB to POV File Converter & Visualizer
- PEDconvert – Convert PLINK PED files into Multiple Genes File Format
- ConverThor 0.2 – Format Conversion between MODICOS and NTS formats
- AFLP convert 0.4 – Format Conversion from AFLP-SURV program to DFDIST program
- Phylo3D 1.2 – Convert Phylogenetic Trees File into LibSea format
- CleanUP – Remove Redundancies from Nucleotide Sequence Databases
- Genbank_to_Fasta 1.1 – Genbank/EMBL to FASTA Conversion Tool
- GenBank2Treedyn 21 – Extract Annotations from GenBank Files
- ALTER 1.3.1 – ALignment File Format Converter
- ExpressConverter 2.1 – Microarray Data Files Transformation Tool
- Convert2Sbml / Convert2Matlab – Convert Metabolic Network Source files into SBML / MATLAB files
- SMArrT – Normalisation of Expression Data in Files
- RC – Reverse/Complement
- Fas2Nex – .FAS to .NEX converter
- SDSW 0.03 – Sliding Divergence Sequence Window
- TAXNAMECONVERT 2.4 – Rename Sequence and Taxon names in Tree and Sequence files
- GTOOL 0.7.5 – Transform Sets of Genotype Data for use with SNPTEST and IMPUTE
- DarwinXporter 0.1.3 – Export Diversity Analysis data for Darwin from Excel data sheets
- convertimpute – Convert IMPUTE format to MultiPhen format
- mega_nexus 1.0 – Convert MEGA input files to Splitstree input files
- xmfa2struct – Converts files in eXtended Multi-Fasta format into Structure file
- LTQ_Profile2Centroid 1.0 – Convert Profile Mod Spectrum data into Centroid Mode Spectrum data
- med2bib 1.04 / toc2bib 1.04 – MEDLINE and TOC/DOC to BibTeX Conversion
- GenCompress 20080118 / GenDecompress – Compression / Decompression for DNA sequences
- PED2SPL 1.4 – Convert standard LINKAGE input files to SPLINK and TRANSMIT
- splitPed / splitRef – Split Pedigree file / Reference Haplotype into smaller files with subsets of markers
- prob2plink 0.01 – Converts MaCH prob+info output to PLINK dosage file
- g2h.pl / h2g.pl / h2h.pl – Convert Genotypes/Haplotypes File
- Linkprep 2.9 – Create LINKAGE style files from AGRF style data
- Html4blast 1.7a – Text to HTML Blast Results Formatter
- Treecon-Tools 0.1 – Convert Phylogenetic Trees File Formate
- pdb2cif 2.4.2 – Cnvert from PDB format to mmCIF
- cif2pdb 2.0.3 – Convert mmCIF to Pseudo-PDB Format
- MEG2DIST – Compute Ecological Indices for Multiple Metagenomic Datasets
- CleanCollapse 1.0.5 – Transfer Alignment of Sequences into Single Sequence
- abi2xml 1.2 – Convert Abi Trace File to Xml File
- Vised 1.1 – Sequence Editor / Display Software
- ORFer 1.3.2.2 – Retrieval of Protein Sequences and Open Reading Frames from GenBank
- APSC 1.0 – Convert Protein Sequence File Format
- XML2PDB – Extract PDB file from XML Structure File
- TABLE 1.9 – Convert Output from Linkage Analysis to more Readable Form
- Haplotyper 1.0 – Genotype Format Data from an Excel File to a Format of Arlequin
- Translate.wdgt – DNA/Protein Conversions
- Readseq 2.1.30 – Read & Reformat Biosequences
- ABI2FASTA 1.1.2 – ABI to FASTA converter
- Yammp Conversion Tools – Simulation of Yammp Models in CHARMM or Amber
- AmberFFC 1.3 – Convert Force Fields for use with Commercial Molecular Modeling Packages
- AlScript 2.0 – Format Multiple Sequence Alignments in PostScrip
- eGATU – easy Genome Annotation Transfer Utility
- GATU – Genome Annotation Transfer Utility
- Mage2Tab 0.9 – MAGE-ML to MAGE-Tab converter
- Tab2MAGE 2.2.2 – Generate MAGE-ML from MAGE-TAB Document
- Vect 1.01 – Visual Extraction & Conversion Tool
- SBML Converters 20100413 – Conversions to & from SBML
- MathSBML 2.10 – working with SBML in Mathematica
- KEGG2SBML 1.5.0 – Convert KEGG Pathway Database to SBML
- SBML2SMW 1.0 – Extract Celldesigner Model to Semantic Mediawiki
- Import Notes 1.1 – CellDesigner Plugin, Import Notes Data from CSV File
- Exceltranspose – Convert Excel File to Genetic Software Fomat File
- ALFmap 1.22 – Convert ALF Format File into Bitmap File
- PDBCNS 2.0 – Interconvert Atom Names between PDB & CNS formats
- Remediator 1.60 – Convert PDB Files between PDBv2.3 & PDBv3.2 Formats
- KinImmerse 0.5 – Translate Kinemage Files into Software for Virtual Environment
- Prekin 6.51 – Prepares Kinemages Files from PDB-format Files
- PovChem 2.1.1 – Chemical Visualization & Illustration & POV File Converter
- REDUCK 1.0 – Remove Duplicates
- GODACK 1.0 – Good Data
- FRICK 1.1 – Filter/Retrieve IDs
- FLICK 1.1 – PCL File Linker
- CCACK 1.0 – Constant Cutoff Analysis
- GAL File Generator 1.2 – Well Plates Files Conversion
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