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Software C++ class library for interpreting data files in NEXUS format. NEXUS Class Library software package is collection of C++ classes designed to simplify interpreting data files written in the NEXUS format used by many computer programs for phylogenetic analyses.NEXUS format allows different programs to share the same data files, even though none of the programs can interpret all of the data stored.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software library that implements lightweight suffix array construction algorithm. Provides C API to construct suffix array and Burrows-Wheeler transformed string from given string over constant size alphabet. The algorithm runs in O(n log n) worst-case time using only 5n+O(1) bytes of memory space, where n is the length of the string.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software C/C++ (and Python) library for sequence alignment using edit (Levenshtein) distance.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software collection of data structures and algorithms. Contains I/O classes (single byte and UTF-8), bitio classes (input, output and various forms of bit level manipulation), text indexing classes (suffix and LCP array, fulltext and minute (FM), ...), BAM sequence alignment files input/output (simple and collating) and many lower level support classes.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software Java library of data structures and algorithms.Provides some basic data structures and algorithms used by SplitsTree, Dendroscope and MEGAN.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software library for processing of biomedical signals. Provides generic storage for biosignals, such as EEG, ECG, MEG. C++ implementation of GDF - " general dataformat for biosignals" version V2.20.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software Fast Analysis of Sequences Toolbox (FAST) is a set of UNIX utilities (for example fasgrep, fascut, fashead and fastr) that extends the UNIX toolbox paradigm to bioinformatic sequence records.FAST workflows are designed for serial processing of flatfile biological sequence record databases per-sequence, rather than per-line, through UNIX pipelines. The default data exchange format is multifasta (specifically, a restriction of BioPerl FastA format). FASTQ format is supported. FAST is designed for learnability, interoperability, interface consistency, rapid prototyping, fine-tuned control, and reproducibility. FAST tools expose the power of Perl and BioPerl to users in an easy-to-learn command-line paradigm.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Relational database schema that underlies many GMOD installations. It is capable of representing many of the general classes of data frequently encountered in modern biology such as sequence, sequence comparisons, phenotypes, genotypes, ontologies, publications, and phylogeny. It has been designed to handle complex representations of biological knowledge and should be considered one of the most sophisticated relational schemas currently available in molecular biology. The price of this capability is that the new user must spend some time becoming familiar with its fundamentals.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software C library for entropy measurement of byte streams and other data.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software library for generic access to chipcard readers and cards

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software object for calculation of multiple sequence alignment from set of unaligned sequences or alignments using the TCoffee program.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software package used to parse output from the PAML programs codeml, baseml, basemlg, codemlsites and yn00. You can use the Bio-Tools-Run-Phylo-PAML modules to actually run some of the PAML programs, but this module is only useful to parse the output.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software Perl extension for reading and writting SCF sequence files.This module provides Perl interface to SCF DNA sequencing files. It has both tied hash and an object-oriented interfaces. It provides the ability to read fields from SCF files and limited ability to modify them and write them back.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software package for performing multiple sequence alignment from set of unaligned sequences and/or sub-alignments by means of the clustalw program.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software Perl interface to SamTools library for DNA sequencing.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software C++ library for parsing several formats in bioinformatics. C++ header only parsing library for several bioinformatics formats (FASTA/Q, MHAP/PAF/SAM), with support for zlib compressed files.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software package which interacts with and retrieves data from NCBI's eUtils. This distribution encompasses low-level API for interacting with (and storing) information from NCBI's eUtils interface. See Bio::DB::EUtilities for the query API to retrieve data from NCBI, and Bio::Tools::EUtilities for the general class storage system. Note this may change to utilize the XML schema for each class at some point, though we will attempt to retain current functionality for backward compatibility unless this becomes problematic.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software application used for working with various biological coordinate systems. See Bio::Coordinate::Collection and Bio::Collection::Pair for examples.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software memory efficient bioinformatics library written in D programming language whose aim is to provide platform for developing high performance computational biology applications using the D programming language through automatic parallelization of tasks where possible and by avoiding unnecessary memory allocations.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software package to generate GD images of Bio::Seq objects.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth