eGPS Desktop

eGPS 1.9 (Latest) 2021/05/14
New features:
Improved the plug-in development guide and added a step-by-step development example.
Fixed the problems in the Venn diagram module and added a Plain text info panel in this module.
Added Tanglegram module to compare two trees.
Added a calculate distance matrix button in Maf operator module.
Updated the Coronavirus GenBrowser plug-in, fixed the display problem of amino acid mutations of frameshift mutations.

eGPS 1.7 2020/11/27
New features:
Added new functions for plug-in(module) "Coronavirus GenBrowser(CGB) 1.0".
Added Classic Skyline plot module.
Add the Bed merger module.
Add an Initialize button in Alignment Trimmer module to help users select a sequence as a reference sequence.
Make a modification to make all modules independent. Transform the module that need user to drag the file into the main interface to open into a module that can be opened independently. Enables users to quickly find the required functions they need in the iTools menu bar.
Fixed bug:
When processing VCF files, merging overlapping BED records before using include Bed and exclude Bed functions.

eGPS 1.6 2020/08/12
New features:
Added new module "Coronavirus GenBrowser 1.0" as a plug-in.
The data panel displays more detailed basic information about the data format, making it smarter to determine the data type.
Added the MA Plot module, which supports displaying the scatter plot of the original data and the scatter plot after log transformation.
Added the function of ringing in the heat map.
Added Alignment trimmer module.
Added VCF to SNP data module.
Added Stairway plot module.
Improve the plug-in mechanism, and add a tutorial on how to develop eGPS plug-ins in eclipse.
Fixed bug:
Text editor fixes the problem that continuous search cannot be performed.
The text editor has added a monospace font, which makes it easy to view MSA data.

eGPS 1.0.5 2019/12/16
New features:
Add Venn diagram painting module, including data input panel, traditional Venn diagram and Upset diagram.
Adjust the behavior after the Build tree button, the parameters are placed in the corresponding tab instead of global setting panel (Preference).
Add global font setting options, currently supports partial font changes.
Replace new icons in the Toolbar to express meanings clearer.
For UTF-8 encoded text files, when the suffixes do not match our standard, add the function of determining the format based on its content. The first successfully judged format will be assigned as current format.
Added editor module capable of opening large text file.
Fixed bug:
When using the heat map module and the row names are not displayed, the legend will stick to cells.
VCF snapshot button on TOOLS is enabled incorrectly.
The control panel of the heat map is not all visible on some computers.
The result of KMeans++ algorithm will be random in heatmap module.

eGPS 1.0.4 2019/11/08
New features:
Added highly interactive heatmap module.
When exporting file successfully, all the software modules record the saved file path.
For each module's tab page, add a close button when module is not focused.
The alignment viewer module adds the Layout parameter bar and adds the InterLeaved layout.
During the software initializing, the eGPS logo will be displayed.
Fixed bug:
After clicking Apply and Close in Preferences, the data is not refreshed.
When the import file has no information to display, clicking on the rectangle box in the data area will incorrectly load the information on the information area.
The module of VCFTools can’t input decimals in the Max missing and HWE box.

eGPS 1.0.3 2019/09/12
New features:
Display the information of the imported file on the information area. Data types include Multiple sequences (MS), Genetic distance (DIST), Phylogenetic tree (TREE), NEXUS, and Population history model (SIMU).
Multiple genetic distance matrixes can be calculated by resampling (bootstrap) and exported for bootstrap analysis.
Build genome tree directly from VCF files.
Replace OTU names in the tree viewer module with batch mode.
Ambiguous nucleotide bases (Nucleotide ambiguity code) are considered when calculating the genetic distance. Two options (i.e. ambiguous base as gap / ambiguous base with equal possibility) are provided.
When importing multiple MSA files of the same type, batch operations are supported. 1) Multiple alignment viewer modules will be opened up and other subsequent analysis can be employed respectively; 2) When using the multiple-sequence aligner, all fasta files will be aligned.
Fixed bug:
A green portable version (i.e. zip package) on the windows system.
The robustness of the MAP analysis is enhanced.
Fixed a problem with the SNJ tree reconstruction method.
Fixed the NaN problem in distance view model.

eGPS 1.0.2 2019/07/26
New features:
Genetic distance viewer module adds new display mode of heat map for enhanced visualization, and support for exporting vector graphics.
In alignment viewer module, exporting NEXUS format file is supported.
For alignment viewer module, loading large file in short time is permitted.
In the evolution analysis, add new features to jump between modules, for example: from the Alignment viewer to the Distance viewer and the Tree viewer.
Provides green, free installation version for MAC OS.
Fixed bug:
Fix the Neuxs file format parse problem, now supports tree and data block.
In the history root node, when you click the right mouse button to mark, a null pointer error occurs.
When dragging an error file, two dialogs will pop up twice.
When the MSA is exported to, for example, the Phylip file format, since the officially defined format is that the sequence noun cannot exceed 12 characters, it is now changed to a loose format.
Some data is not suitable for DEG-MassSpecturm module to analyze, add a dialog to tell users.

eGPS 1.0.1 2019/07/09
New features:
Increase Alignment View export format, now we support ClustW/ GCG(MSF)/MEGA/PAML/ PHYLIP.
Add new module geneToAlignment, reconstruct the codes of geneToAlignment/geneToDistance/ geneToGenetree.
Update user manual.
Add Log.
Add new module multiple sequence aligner which package two programs : ClustalW and Mafft.
Add new options when obtaining alignment, calculate Genetic distance and infer phylogenetic tree from gene symbol: 1. whole gene body length 2. exons 3. introns 4. coding sequence 4. 4-fold degenerate sites.
Add new options for Genetic distance: The transversion rate. When obtaining alignment of 4-fold degenerate sites, 4DTv rates (the rate of transversion at fourfold degenerate sites) could be computed.
Fixed bug:
considered gene regions not wok for exons
For swingx jar library: JXTaskPanel in MAC OS is grey.
Alignemnt View display problem.
These are two dialog when files in Recent file have been deleted
When save GeneToGeneticDist file in distance viewer, the number of OUT is not correct.