Citation: Zeng XY, Tan TJ, Tian FH, Wang Y, Wen TC (2023) OFPT: a one-stop software for fungal phylogeny. Mycosphere, 14(1): 1730–1741. https://doi.org/10.5943/mycosphere/14/1/20
Copyright: No. 2023SR1445017 (2023-07-27)
Introduction
OFPT is a powerful software that provides the following features:
Download sequence
Sequence alignments
Trim alignments
Concatenate alignments
Modeltest
Convert format
Construct ML tree
Construct Bayesian tree
If any technical problem, you are welcomed to contact: xyzeng3@gzu.edu.cn
There is now no limitation in quantity when downloading sequences.
Merged the 'check' function in 'Download sequence'.
Updated the content in 'help'.
Updated the 'setting' function, where global strategies for aligning and trimming are always '0'.
Added one-click mode.
Some structural changes in coding.
V1.8.2 2023-11-01
Fixed a bug of internet checking.
V1.8.1 2023-10-28
Added the process of internet checking.
Added citation information.
V1.8.0 2023-09-22
Added the function to check updates when running the program.
Improved the instructions and UI.
Changed the trimming methods.
Increased the parameter 'ngen' from 5,000,000 to 50,000,000 in MyBayes command block.
Added system information in 'Information.txt'.
V1.7.1 2023-07-31
Fixed the bug of writing the MrBayes' block when gamma categories are large than 10.
V1.7 2023-07-27
Fixed the bug that the program will quit after using the function 'h', 'c' and 's'.
Added the results of SH-like approximate likelihood ratio test (SH-aLRT) for constructing ML tree.
Now the program will record error information in the 'Information.txt'.
Improved some functional descriptions.
Improved the structure of the program.
Added the verification for users' sequence data.
V1.6 2023-07-25
Improved the descriptions and hints in the software.
Added the function to record the time when running each module.
Improved the verifying algorithm of accession numbers.
Changed the structure of the program, making the <out> folder generate only final files.
The ‘Information.txt' file will now generate in the <out> folder too.
Fixed the bug when space is included in the accession numbers.
V1.5 2023-07-15
Fixed more bugs when specifying aligning strategies and trimming mode for different strategies.
Allowed the users to use a single hyphen or en-dash, besides empty cells, to represent missing accession numbers.
Some small changes on UI.
Added the function to replace illegal characters in users' sequence ID to underscores.
Changed the output directory of '.html' files generated by trimming module form folder 'temp' to 'in'.
Removed the generation of 'Partition.txt', and moved its information to a new output file 'Information.txt' in the working directory, in which will record the information for each step.
Specified the datatype to 'string' when reading then excel.
V1.4 2023-07-12
Fixed the bug when specifying aligning strategies and trimming mode for different strategies.
Added the .html files as the outputs after trimming, so that users can see the columns/sequences that trimAl maintains in the new alignment.
Updated the options of trimming methods.
Updated the contributors' list.
Fixed the bug in the function 'check' when the column of 'Reference(s)' exist.
V1.3 2023-07-11
Changed back from 'input' to 'print' if user data of a gene does not exist.
Allow users to have the column named 'Reference(s)' when reading accession numbers in the 1st sheet.
Added the trimming method of 'strict' and updated its description.
Updated the content in 'help'.
Added functions of applying different strategies and modes for aligning and trimming to different genes.
V1.2 2023-07-08
Raised an error if identical sequence ID occur when concatenating.
Changed 'print' to 'input' when error occurs.
Fixed fatal bugs when reading headers with illegal characters in sheet1.
Made error messages more obvious.
Added the function for checking accession numbers.
Replaced the option of quit program to check accession numbers.