Trimming trees with TreeBeST

Posted: 2020-01-18 | Author: | Filed under: academic | Tags: , , , , , | Leave a comment

I needed a program that can easily trim branches from a phylogenetic tree and came across TreeBeST (Tree Building guided by Species Tree). TreeBeST is a neat and versatile program that builds, manipulates and displays phylogenetic trees and seems to be perfect for the job.
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Archaeopteryx configuration 2

Posted: 2019-01-29 | Author: | Filed under: academic | Tags: , , , , | Leave a comment

Couple of years ago, I wrote about the configuration file of Archaeopteryx, a phylogenetic tree analysis program. I have set it to use native ui, as described in my old post. However, some things have changed meanwhile, so in order to have a white background, additional tweaks are required.
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Cleaning up with sed

Posted: 2017-03-31 | Author: | Filed under: academic | Tags: , , , , , , | Leave a comment

I needed to clean up some plain text files from data and characters I did not want.

To be more precise, I have a phylogenetic tree, obtained from the TimeTree web-site. Species presented there are mainly birds, several reptiles and a fish. The tree has branches length information and node labels, which I wanted to remove.
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Archaeopteryx configuration

Posted: 2016-09-30 | Author: | Filed under: academic | Tags: , , , , | 1 Comment

Archaeopteryx is a software tool for the visualization, analysis, and editing of potentially large and highly annotated phylogenetic trees. It is available at SBo and is particularly useful if you want to create visually appealing phylogenetic trees, to be used for publication figures or presentation slides. One thing that I do not like is that by default, the program has black interface and black background. Read the rest of this entry »