Open Source Perl Bio-Informatics Software
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Perl Bio-Informatics Software
View 58 business solutionsBrowse free open source Perl Bio-Informatics Software and projects below. Use the toggles on the left to filter open source Perl Bio-Informatics Software by OS, license, language, programming language, and project status.
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Boost Partnership Revenue and Engagement in minutesIntrow is a next-gen Partner Relationship Management (PRM) platform built to seamlessly connect, engage, and grow your partner ecosystem—all while keeping your CRM as the single source of truth.
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A role-based, highly configurable module for managing merit, promotions, bonuses, and stocks.FocalReview®, SpiraLinks’ flagship tool, helps you manage your compensation planning and performance processes more efficiently.
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SAM (Sequence Alignment/Map) is a flexible generic format for storing nucleotide sequence alignment. SAMtools provide efficient utilities on manipulating alignments in the SAM format. The main samtools source code repository moved to GitHub in March 2012. For ongoing development since then, see http://github.com/samtools/samtools
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MUMmer is a modular system for the rapid whole genome alignment of finished or draft sequence. This package provides an efficient suffix tree library, seed-and-extend alignment, SNP detection, repeat detection, and visualization tools.
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A set of tools for working with VCF files, such as those generated by the 1000 Genomes Project. This project is migrating to github: https://vcftools.github.io/
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Systems Biology Markup Language (SBML)
A file format for exchanging computational models in systems biology
The Systems Biology Markup Language (SBML) is an XML-based description language for representing computational models in systems biology. Visit the project web site to learn more. -
Epicor BisTrack is a powerful business management software designed specifically for the needs of the building materials industry, including lumberyards, construction suppliers, and distributors.Epicor BisTrack is a powerful business management software designed specifically for the needs of the building materials industry, including lumberyards, construction suppliers, and distributors. Known for its comprehensive suite of tools, BisTrack streamlines operations by integrating inventory management, purchasing, sales, and delivery processes into a single, user-friendly platform. Its advanced reporting and analytics capabilities enable businesses to make data-driven decisions, optimize workflows, and enhance customer service. With robust mobile functionality and seamless cloud-based deployment options, BisTrack supports real-time collaboration and efficient operations across teams, ensuring businesses stay competitive in a fast-paced industry.
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Design PCR primers from DNA sequence. Widely used (190k Google hits for "primer3"). From mispriming libraries to sequence quality data to the generation of internal oligos, primer3 does it. C&perl. Developers/testers/documenters needed.
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Free DELTA
Software tools for processing taxonomic descriptions in DELTA format
The Free DELTA Project is a free, open-source, software alternative for a generic system to the processing of taxonomic descriptions based on the DELTA (DEscription Language for TAxonomy) format. -
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HaploPainter - a pedigree and haplotypes drawing tool written in Perl/Tk. The software processes pedigree information in standard linkage formats combining haplotype information outputs from Simwalk, Genehunter, Allegro and Merlin.
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PerlPrimer is a GUI application written in Perl that designs primers for standard PCR, bisulphite PCR and Real-time PCR (QPCR). It aims to automate and simplify the process of primer design.
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The Sashimi project hosts the Trans-Proteomic Pipeline (TPP), a mature suite of tools for mass-spec (MS, MS/MS) based proteomics: statistical validation, quantitation, visualization, and converters from raw MS data to the open mzML/mzXML formats.
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Digital Adoption and User Training - in one solutionClickLearn captures work processes in enterprise software - and auto-produces learning content in 7 formats and 45 languages, creates a customisable e-learning portal and keeps documentation current with automatic updates.
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Integrated Hospital Information System. PHP,mySQL,PostgreSQL. Surgery, Nursing,Outpatient,Wards,Labs, Pharmacy, Security,Admission,Schedulers, Repair, Communication & more. Multilanguage, WYSIWYG forms, userconfig, embedded workbots. Modular & scalab
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FSA is a probabilistic multiple sequence alignment algorithm which uses a "distance-based" approach to aligning homologous protein, RNA or DNA sequences.
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A bioinformatics tool to PRe-process and show INformation of SEQuence data. The tool is written in Perl and can be helpful if you want to filter, reformat, or trim your sequence data. It also generates basic statistics for your sequences.
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proTRAC
Use proTRAC to annotate genomic piRNA clusters
proTRAC detects genomic piRNA clusters. It considers all the relevant features of mapped sequence reads like the amount of 1U/10A, size and strand bias to ensure a high specificity. -
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GPL-licensed Electronic Medical Record and Practice Management system for medical providers that runs in any web browser in multiple languages. It provides an XML-RPC backend and multiple import and export formats, as well as reporting and other features
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FragGeneScan is an application for finding (fragmented) genes in short reads. It can also be applied to predict prokaryotic genes in incomplete assemblies or complete genomes. FragGeneScan was first released through omics website (http://omics.informatics.indiana.edu/FragGeneScan/) in March 2010, where you can find its old releases. FragGeneScan migrated to SourceForge in October, 2013.
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AMOS
AMOS is a collection of tools for genome assembly
AMOS is a collection of tools and class interfaces for the assembly of DNA reads. The package includes a robust infrastructure, modular assembly pipelines, and tools for overlapping, consensus generation, contigging, and assembly manipulation. -
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Celera Assembler (CA) is a whole-genome shotgun (WGS) assembler for the reconstruction of genomic DNA sequence from WGS sequencing data.
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[DEPRECATED] Gene Ontology
The DEPRECATED legacy location of the GO, see http://geneontology.org
The DEPRECATED legacy of the Gene Ontology project on SourceForge. Please see http://geneontology.org for current software and downloads. -
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scalpel
Genetic variants discovery tool
Bioinformatics pipeline for discovery of genetic variants from NGS reads. -
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MaxBin
An automatic tool for binning metagenomics sequences
MaxBin is a software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm. Users could understand the underlying bins (genomes) of the microbes in their metagenomes by simply providing assembled metagenomic sequences and the reads coverage information or sequencing reads. For users' convenience MaxBin will report genome-related statistics, including estimated completeness, GC content and genome size in the binning summary page. Users could use MEGAN or similar software on MaxBin bins to find out the taxonomy of each bin after the binning process is finished. The most current version is 2.2.7. MaxBin was published on Microbiome journal (2:26)! Please cite the Microbiome paper if you use MaxBin in your work. -
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czplib
Chaolin Zhang's Perl Library
Chaolin Zhang's Bioinformatic Perl Library -
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BioC
We describe a simple XML format to share text documents and annotation
A minimalist approach to share text documents and data annotations. Allows a large number of different annotations to be represented. Project files contain: - simple code to hold/read/write data and perform sample processing. - BioC-formatted corpora - BioC tools that work with BioC corpora BioC goals - simplicity - interoperability - broad use - reuse There should be little investment required to learn to use a format or a software module to process that format. We are interested in reuse, and we focus on common NLP tasks that are broadly useful for textmining. -
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Source code from the Research Institute for Signals, Systems and Computational Intelligence http://fich.unl.edu.ar/sinc
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MitoSAlt
Identification of mitochondrial structural alterations
MitoSAlt is a pipeline to identify large deletions and duplications in human and mouse mitochondrial genomes from next generation whole genome/exome sequencing data. The pipeline is capable of analyzing any circular genome in principle, as long as a proper configuration file is provided. -
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The Simplest Manual Counter
Manual counter with the keyboard or the mouse on images
The only open source counter to count any items the simplest and easiest way with the keyboard, or the mouse specifically on images. After associating a key to each item, or a predefined graphical symbol for images, pressing the key or clicking on the image increments its associated counter, and displays (for the images) the symbol at the mouse's pointer location. Such a project is so simple a child could use it!
