Introduction
This course is meant to work with different kinds of alignment programs and tree contruction software.
There is a lot of available software out there, free and paid, but also web portals to do the job.
Web portals, however, are often limited to the size of the data to prevent users uploading gigabytes of data.
Your computer, depending on the physics like cpu, available RAM etc. makes it possible to handle large data sets.
PhyloMain v6, that is available via this website, is using freely available software to do the job.
Much more software on this topic is available on the internet and this website.
Updated version: 2022-08-20
If you already downloaded the package then use the next download to update the PhyloMain program:
Create a folder .e.g. D:\PhyloMain. Move the zip file into this folder and unzip the file here. A folder PhyloMain is created that contains the starting program and the subfolders Examples, Manual and Progs.
Move the subfolder Progs to C:\Users\Public (in Dutch: C:\Gebruikers\Openbaar).
In D:\PhyloMain start the program by double-clicking PhyloMain.exe; there is a newer version available down at this webpage. It offers some benefits.
When everything is correct, you will see this window appearing on your monitor.
Comments and questions can be addressed via contact form.
Assign programs, that are used in PhyloMain
In case you didn't move the 'Progs' folder to C:\Users\Public, you have to assign every single program to the new directory.
E.g. if the 'Progs' folder is still in the installation folder then 'progsdir' should become D:\PhyloMain\Progs
Double-click on the specific program and choose the right folder and program; some are .exe files, others .bat
Look at the examples in the window:
bioedit = C:\Users\Public\Progs\BioEdit\BioEdit.exe and should be changed into D:\PhyloMain\Progs\BioEdit\BioEdit.exe
mafft = C:\Users\Public\Progs\mafft-win\mafft.bat should be changed into D:\PhyloMain\Progs\mafft-win\mafft.bat
and so on.
