:: DESCRIPTION
Pysam is a python module for reading and manipulating Sam files.
::DEVELOPER
Computational Genomics: Analysis and Training (GCAT)
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: MORE INFORMATION
:: DESCRIPTION
The program gffread can be used to validate, filter, convert and perform various other operations on GFF (General Feature Format) files.
::DEVELOPER
The Center for Computational Biology at Johns Hopkins University
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Pertea G, Pertea M.
GFF Utilities: GffRead and GffCompare.
F1000Res. 2020 Apr 28;9:ISCB Comm J-304. doi: 10.12688/f1000research.23297.2. PMID: 32489650; PMCID: PMC7222033.
:: DESCRIPTION
vcflib is a simple C++ library for parsing and manipulating Variant Call Format (VCF) files, + many command-line utilities
::DEVELOPER
Erik Garrison erik.garrison@bc.edu
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
BiopLib is a library of C routines for general programming and handling protein structure
BiopTools is a set of command line tools written in C and making use of the BiopLib library for manipulation of protein structure and sequence
::DEVELOPER
Andrew C.R. Martin’s Bioinformatics Group at UCL
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
BiopLib and BiopTools – a C programming library and toolset for manipulating protein structure.
Porter CT, Martin AC.
Bioinformatics. 2015 Aug 30. pii: btv482.
:: DESCRIPTION
PDBest (PDB Enhanced Structures Toolkit) is a freely available platform for manipulating, filtering and normalizing biomolecules in Protein Data Bank (PDB) and mmCIF structure files.
::DEVELOPER
PDBest team , the Bioinformatics and System Laboratory (LBS) at Universidade Federal de Minas Gerais, Brazil.
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
PDBest: a user-friendly platform for manipulating and enhancing protein structures.
Gonҫalves WR, Gonҫalves-Almeida VM, Arruda AL, Meira W Jr, da Silveira CH, Pires DE, de Melo-Minardi RC.
Bioinformatics. 2015 Apr 24. pii: btv223
:: DESCRIPTION
The dbtoolkit application enables easy manipulation of fasta sequence database in a user-friendly environment. Sequence databases can be merged, shuffled, truncated, etc… Furthermore, for more experienced users, the Java API provides a well documented and easy-to-use environment for customized fasta database manipulations.
::DEVELOPER
Computational Omics and Systems Biology Group
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Martens et al.
DBToolkit: processing protein databases for peptide-centric proteomics.
Bioinformatics (2005) vol. 21 (17) pp. 3584-5
:: DESCRIPTION
mozCellML is a Mozilla based CellML tool. It can be used to edit boundary conditions, integrate models(using a Runge-Kutta method), and fit parameters to models(using Levenberg-Marquardt).
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
