A more complete list of MSA viewers is available on the web at CLC Viewer is a recent free package written in Java which contains a number of integrated tools and acts as a core product for adding other features through a commercial version. Like early versions of CINEMA, PFAAT is implemented in Java for operating system independence. More recent developments include the Protein Family Alignment Annotation Tool (PFAAT)ġ2 designed specifically for family analysis and incorporating residue annotation tools as well as integration with Jmol for protein structure display. Clustal Omega is the most recent version, but at the time of writing only has a command line interface - a beta version of a GUI is due to be released soon. It has now been rewritten in C++ and is part of UTOPIAġ1, a GUI for the ClustalW multiple sequence alignment program, providing an integrated environment for aligning sequences and analyzing results. CINEMAħ was probably the first sequence alignment viewer and editor implemented in Java, a platform independent programming language allowing graphical user interfaces (GUIs) to run on any operating system. A problem in writing graphical software is the operating-system dependency of many graphics libraries. Other early viewers include GeneDocĥ which is part of the RnaViz package for visualizing RNA secondary structuresĦ, but which can be used for protein sequence alignments. Neither seems to be actively maintained or easily available any more. These range from tools which provide attractive printed outputs, through standalone graphical tools - either operating-system dependent, or independent - to web-based viewers.Ģ written for VAX/VMS workstations. As a result, there are a plethora of tools for viewing MSAs. ĬLC bio maintains a scientific focus by initializing and participating in various research projects around the world, including multiple projects funded by grants.Viewing multiple sequence alignments (MSAs) is a fundamental requirement in the analysis of protein sequences, allowing us to visualize conservation across protein families as well as unusual features of particular sequences. 30% of the employees have a PhD and another 50% have a MSc. It is a profitable, privately owned company with 100 employees and has been acquired by Qiagen in late 2013. CLC bio is no longer developing their own hardware-based products.ĬLC bio started commercial activities on Januheadquartered in Denmark. Hardware Įarly on, the company presented own-developed high-performance computing solutions, focusing on accelerating open source algorithms such as HMMER, Smith-Waterman and ClustalW, using FPGA technology. In 2020, CLC bio released a free plug-in that enables workflow execution on AWS directly from the CLC Genomics Workbench desktop software. In 2019, this platform was adapted for and approved for use in AWS GovCloud. In 2017, CLC bio launched their CLC Genomics Cloud Engine as a command-line driven platform for cloud-based bioinformatics workflow execution on Amazon Web Services. ![]() The platform includes both a desktop graphical user interface, command-line tools, a SOAP and REST API, and the ability to run containerized tools.ĬLC bio's analysis platform has been installed at several of the world's research institutions and at more than 2000 different organizations around the globe, including the top 10 pharmaceutical companies in the world. CLC bio's software is platform independent and can be used for Mac OS X, Windows, and Linux. CLC bio also provides additional plugins (both free and commercial) that extend the platform for use in specific subject areas including genome finishing, microbial genomics, and structural biology.ĬLC bio's software allows the user to analyze, visualize, and compare genomic, transcriptomic, and epigenomic data from all major high-throughput sequencing platforms such as Illumina, Life Technologies, Roche 454, Pacific Biosciences, Oxford Nanopore, and Complete Genomics. Īmong other features, the software supports read mapping of Sanger and high-throughput sequencing data, de novo assembly of Sanger and high-throughput sequencing data, SNP detection on whole genomes of any size, detection of structural variations on whole genomes of any size, ChIP-seq analysis, RNA-Seq analysis, small RNA analysis and BLAST. In 2010, CLC bio was the first commercial platform for bioinformatics analysis that utilized a graphical user interface for building, managing, and deploying analysis workflows. While offering some open source algorithms with their tools, CLC bio have their own implementations of several popular applications, which have been accelerated using SIMD technology. ![]() CLC bio develops widely cited desktop, enterprise and cloud software for analysis of biological data.
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