The Newick-Tree-Modifier (NTM) is a small application that prunes specifically predesigned or uploaded Newick master trees (including all available species in an up-to-date phylogenetic order) corresponding to user-designed FASTA sequences or species lists, keeping the correct phylogenetic order in Newick format. NTM can also graphically modify the general tree topology, e.g., by "copy and paste," to subsequently test different phylogenetic hypotheses.

In the input section you can select/enter your data and submit for calculation. You can also extract species from newick trees and directly convert sequence data to other formats. The input section looks: At the bottom of the views, there is a message line, where messages and errors are printed.

Title	Description
Download Name	A name (praefix) of the output/result files. Default is the name of the uploaded FASTA/species or the "ntm" prefix plus date and time.
Newick Tree - upload, select or enter	Upload your own newick tree, select a predefined master tree (from the server) or enter a master tree manually. You have the option to download the Newick tree (may be interesting for the predfined ones), or select species from the uploaded / selected tree, which can be entered in the text part of the sequence or species section below.
Sequences or Species - upload, select or enter	Upload, enter your species or sequence data. Species must be entered one by one on different lines. With the three buttons "FASTA", "NEXUS" and "PHYLIP" you can convert "on the fly" you sequence data to other formats and download it.
Reformat to acronyms	e.g., hom_sap
Delete redundant species	Reduce all sequences to one per species
Output control (ctl) file for paPAML	Creates a specific control file for paPAML containing the name of a Newick tree and FASTA file.

A testcase for FASTA and Species list inputs can be applied to lysozymes of primates. The corresponding master tree (MastaMammalia) is automatically selected.

This dialog lets you select species from a newick tree.

Symbol or Title	Description
◼	Mark all VISIBLE elements in the box
◻	Unmark ALL elements in the box
▼	Move all selected elements in the "Selection" box.
▲	Move all selected elements in the "Available" box.
▶	Apply the entered pattern and display only the species which matches. This does not effect any selection done so far, it only limits the visible elements.

On the right displayed tree you can click on nodes (or leaves) and they are put in the "Selected" box on the other side.

After a successful run, the results control panels are visible.

„Edit: Treegraph 2” offers a graphical view of the pruned tree and enables one to download or edit the tree topology within the TreeGraph 2 application.

For TreeGraph 2, you need a running Java environment on your local computer.

Note: you may have to specify the website "http://retrogenomics.uni-muenster.de" as trust worthy in the Privacy "Exception List" - e.g., For Mac this is in the System Preferences: Security&Privacy: Open Anyway.

All manipulations, e.g., delete and cut-and-paste branches, are allowed. Finally, label the modified tree and go to File: export to tree format Newick file that will export the modified Newick tree to your computer.