Tree of archeaplastida TAP proteins for family: PcG_MSI
Method used for alignment generation: Mafft-FFTNSI
The alignment can be downloaded here and the tree can be downloaded using the Archaeopteryx interface.
All alignments were modified by two TrimAl iterations if not stated otherwise. First, the option "-automated1" was used and afterwards, the sequences in the alignment were filtered using "-resoverlap 0.75 -seqoverlap 50". Phylogenetic trees were inferred using quicktree_sd with 100 bootstraps.
A list of lettercodes included in the protein names can be found here (opens in new tab).
Some species like Boechera stricta and Marchantia polymorpha (genome) were not included into the tree inference because they were not published at the time the calculations were performed.
To visualize the tree Archaeopteryx.js was used. For more information on how to use it see its documentation.
Quick use: mouse scroll bar to zoom into/out of the tree; CTRL+F or menu to search for sequences; menu to change labeling. If the menu is not placed correctly, you can drag and drop it as you need it.
It can take a couple of seconds to load the tree.