The Experts below are selected from a list of 2556 Experts worldwide ranked by ideXlab platform
Ingo Michalak - One of the best experts on this subject based on the ideXlab platform.
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raxmlgui a Graphical Front End for raxml
Organisms Diversity & Evolution, 2012Co-Authors: Daniele Silvestro, Ingo MichalakAbstract:With the increasing availability of molecular data, maximum likelihood approaches have gained a new central role in phylogenetic reconstructions. Extremely fast tree-search algorithms have been developed to handle data sets of ample size in reasonable time. In the past few years, RAxML has achieved great relevance in this field and obtained wide distribution among evolutionary biologists and taxonomists because of its high computational performance and accuracy. However, there are certain drawbacks with regard to its usability, since the program is exclusively command-line based. To overcome this problem, we developed raxmlGUI, a Graphical user interface that makes the use of RAxML easier and highly intuitive, enabling the user to perform phylogenetic analyses of varying complexity. The GUI includes all main options of RAxML, and a number of functions are automated or simplified. In addition, some features extEnd the standard use of RAxML, like assembling concatenated alignments with automatic partitioning. RaxmlGUI is an open source Python program, available in a cross-platform package that incorporates RAxML executables for the main operating systems. It can be downloaded from http://sourceforge.net/projects/raxmlgui/.
Daniele Silvestro - One of the best experts on this subject based on the ideXlab platform.
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raxmlgui a Graphical Front End for raxml
Organisms Diversity & Evolution, 2012Co-Authors: Daniele Silvestro, Ingo MichalakAbstract:With the increasing availability of molecular data, maximum likelihood approaches have gained a new central role in phylogenetic reconstructions. Extremely fast tree-search algorithms have been developed to handle data sets of ample size in reasonable time. In the past few years, RAxML has achieved great relevance in this field and obtained wide distribution among evolutionary biologists and taxonomists because of its high computational performance and accuracy. However, there are certain drawbacks with regard to its usability, since the program is exclusively command-line based. To overcome this problem, we developed raxmlGUI, a Graphical user interface that makes the use of RAxML easier and highly intuitive, enabling the user to perform phylogenetic analyses of varying complexity. The GUI includes all main options of RAxML, and a number of functions are automated or simplified. In addition, some features extEnd the standard use of RAxML, like assembling concatenated alignments with automatic partitioning. RaxmlGUI is an open source Python program, available in a cross-platform package that incorporates RAxML executables for the main operating systems. It can be downloaded from http://sourceforge.net/projects/raxmlgui/.
Andreas Zeller - One of the best experts on this subject based on the ideXlab platform.
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my program worked. today it does not. why
1999Co-Authors: Andreas Zeller, Universitlt PassauAbstract:Abstract. Imagine some program and a number of changes. If none of these changes is applied (“yesterday”), the program works. If all changes are applied (“today”), the program does not work. Which change is responsible for the fail-ure? We present an efficient algorithm that determines the minimal set of failure-inducing changes. Our delta debugging prototype tracked down a single failure-inducing change from 178,000 changed GDB lines within a few hours. 1 A True Story The GDB people have done it again. The new release 4.17 of the GNU debugger [6] brings several new features, languages, and platforms, but for some reason, it no longer integrates properly with my Graphical Front-End DDD [lo]: the arguments specified within DDD are not passed to the debugged program. Something has changed within GDB such that it no longer works for me. Something? Between the 4.16 and 4.17 re-leases, no less than 178,000 lines have changed. How can I isolate the change that caused the failure and make GDB work again? The GDB example is an instance of the “worked yesterday, not today ” problem
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Yesterday, my program worked. Today, it does not. Why?
1999Co-Authors: Abteilung Softwaretechnologie, Andreas ZellerAbstract:Imagine some program and a number of changes. If none of these changes is applied ("yesterday"), the program works. If all changes are applied ("today"), the program does not work. Which change is responsible for the failure? We present an efficient algorithm that determines the minimal set of failure-inducing changes. Our delta debugging prototype tracked down a single failure-inducing change from 178,000 changed GDB lines within a few hours. 1 A True Story The GDB people have done it again. The new release 4.17 of the GNU debugger [6] brings several new features, languages, and platforms, but for some reason, it no longer integrates properly with my Graphical Front-End DDD [9]: the arguments specified within DDD are not passed to the debugged program. Something has changed within GDB such that it no longer works for me. Something? Between the 4.16 and 4.17 releases, no less than 178,000 lines have changed. How can I isolate the change that caused the failure and make GDB work again?..
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ddd a free Graphical Front End for unix debuggers
Sigplan Notices, 1996Co-Authors: Andreas Zeller, Dorothea LutkehausAbstract:The Data Display Debugger (DDD) is a novel Graphical user interface to GDB and DBX, the popular UNIX debuggers. Besides "usual" features such as viewing source texts and breakpoints, DDD provides a Graphical data display, where data structures are displayed as graphs. A simple mouse click dereferences pointers or reveals structure contents. Complex data structures can be explored incrementally and interactively, using automatic layout if preferred. Each time the program stops, the data display reflects the current variable values. DDD has been designed to compete with well-known commercial debuggers; however, it is free software, protected by the GNU general public license. In this paper, we give a quick presentation of DDD and describe its architecture and basic functionality from a technical point of view.
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ddd a free Graphical Front End for unix debuggers
Sigplan Notices, 1996Co-Authors: Andreas Zeller, Dorothea LutkehausAbstract:The Data Display Debugger (DDD) is a novel Graphical user interface to GDB and DBX, the popular UNIX debuggers. Besides "usual" features such as viewing source texts and breakpoints, DDD provides a Graphical data display, where data structures are displayed as graphs. A simple mouse click dereferences pointers or reveals structure contents. Complex data structures can be explored incrementally and interactively, using automatic layout if preferred. Each time the program stops, the data display reflects the current variable values. DDD has been designed to compete with well-known commercial debuggers; however, it is free software, protected by the GNU general public license. In this paper, we give a quick presentation of DDD and describe its architecture and basic functionality from a technical point of view.
Dorothea Lutkehaus - One of the best experts on this subject based on the ideXlab platform.
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ddd a free Graphical Front End for unix debuggers
Sigplan Notices, 1996Co-Authors: Andreas Zeller, Dorothea LutkehausAbstract:The Data Display Debugger (DDD) is a novel Graphical user interface to GDB and DBX, the popular UNIX debuggers. Besides "usual" features such as viewing source texts and breakpoints, DDD provides a Graphical data display, where data structures are displayed as graphs. A simple mouse click dereferences pointers or reveals structure contents. Complex data structures can be explored incrementally and interactively, using automatic layout if preferred. Each time the program stops, the data display reflects the current variable values. DDD has been designed to compete with well-known commercial debuggers; however, it is free software, protected by the GNU general public license. In this paper, we give a quick presentation of DDD and describe its architecture and basic functionality from a technical point of view.
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ddd a free Graphical Front End for unix debuggers
Sigplan Notices, 1996Co-Authors: Andreas Zeller, Dorothea LutkehausAbstract:The Data Display Debugger (DDD) is a novel Graphical user interface to GDB and DBX, the popular UNIX debuggers. Besides "usual" features such as viewing source texts and breakpoints, DDD provides a Graphical data display, where data structures are displayed as graphs. A simple mouse click dereferences pointers or reveals structure contents. Complex data structures can be explored incrementally and interactively, using automatic layout if preferred. Each time the program stops, the data display reflects the current variable values. DDD has been designed to compete with well-known commercial debuggers; however, it is free software, protected by the GNU general public license. In this paper, we give a quick presentation of DDD and describe its architecture and basic functionality from a technical point of view.
Santanen Jukka-pekka - One of the best experts on this subject based on the ideXlab platform.
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Potku - New analysis software for heavy ion elastic recoil detection analysis
'Elsevier BV', 2016Co-Authors: Arstila Kai, Julin Jaakko, Laitinen Mikko, Aalto Jarkko, Konu Timo, Kärkkäinen Samuli, Rahkonen Samuli, Raunio Miika, Itkonen Jonne, Santanen Jukka-pekkaAbstract:Time-of-flight elastic recoil detection (ToF-ERD) analysis software has been developed. The software combines a Python-language Graphical Front-End with a C code computing back-End in a user-friEndly way. The software uses a list of coincident time-of- flight–energy (ToF–E) events as an input. The ToF calibration can be determined with a simple Graphical procedure. The Graphical interface allows the user to select different elements and isotopes from a ToF–E histogram and to convert the selections to individual elemental energy and depth profiles. The resulting sample composition can be presented as relative or absolute concentrations by integrating the depth profiles over user-defined ranges. Beam induced composition changes can be studied by displaying the eventbased data in fractions relative to the substrate reference data. Optional angular input data allows for kinematic correction of the depth profiles. This open source software is distributed under the GPL license for Linux, Mac, and Windows environments.peerReviewe
