Package: phylo-matt
MATT - A FRAMEWORK FOR MODIFYING AND TESTING TOPOLOGIESTable of ContentsInstallationUsageContributionLicenseCitationContactInstallationMATTis distributed as a python package calledphylo-matt.MATTrequires aPythonversion of 3.8 or higher.Once python and the included package manager are installed,MATTcan be installed using thepipcommand in a
console:pip install phylo-mattIf you run into errors, try:pip install phylo-matt --userUsageLaunchAfterMATThas been installed it can be launched using themattcommand in a console:mattThis will startMATTand openhttp://localhost:5000in the preferred browser.Once openMATTcan be used via the GUI in the browser.To closeMATTafter usage, simply kill the server by hittingCtrl+Cin the console.ImportMake sure to set all the needed options under the "Options" button in the top right corner first.
You will also find a reference to this file there.Afterwards optionally set a session name and import your alignment and/or tree file.
Alternatively you can import the example files.If you do not name the session, default file names will be used and might override older files.If you only import an alignment file, you can letMATTgenerate the tree for you.If you only import a tree file, you will not be able to use all ofMATT'sfeatures.NavigationAfter the tree has been drawn, you can navigate through it:To zoom in, use eitherScrollUpon your input device,
the "Zoom in" button in the top left corner
or the "Zoom in" in the context menu (RightClick).To zoom out, use eitherScrollDownon your input device,
the "Zoom out" button in the top left corner
or the "Zoom out" in the context menu (RightClick).Click & Dragto move the tree around.The minimap in the top right corner shows you the tree and the viewport.Clicksomewhere inside to jump to that location.To search for a specific entry, enter the name in the search in the top left corner and hitEnterorClickthe button next to the input field.Use the buttons "Show/Hide branch lengths" and "Align/Attach labels" in the top right corner
or their versions in the context menu to toggle between the viewmodes for branch lenghts and labels.Changing topologiesClickon a branch to select it. After you have selected a branch you can swap it with another branch,
byClickingthat other branch.After selecting a branch, the "Set Root" button appears.Clickit to set the selected branch as a root.
Alternatively you canRightclicka branch to select it and set the root directly in the context menu.Once you have changed the initial topology, you can "Undo" and "Redo" your changes,
using the buttons in the top left corner or the context menu.Saving and testing topologiesIf you want to save a topology,Clickthe "Save snapshot" button or the option in the context menu.
Optionally you can name the snapshot and then save it.Once a snapshot is saved, you can find it under the "Snapshots" button or in the context menu.
In the snapshots menu you can jump to another snapshot directly, change its name or download it.
Here you can also select multiple snapshots and test them.
After the tests have run, a menu opens up, showing you the test results of the topology tests.ContributionAny bug reports, comments and suggestions are highly appreciated. Pleaseopen an issue on GitHubor contact us viaemail.LicenseMATTis licensed under theGNU General Public License v3.0.CitationAn Application Note is in the works. Stay tuned.ContactFor further support or bug reports please contact us viaemail.