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I am looking to manipulate manually constructed phylogenetic trees (adding bootstrap values, markers to indicate trate loss/gain etc.) I came across a paper that used Macclade, however, this no longer appears to be a program that will run on almost all computers. Is there a useful alternative software package? I have tried Mesquite, but it does not appear to have the same functionality (although, I have probably just missed understood how to use it effectively).

Any help/recommendations would be appreciated

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If you have some knowledge of python, you can do a lot of things with the ETE toolkit.

Disclaimer: I have used an older version of it, but in a very limited manner.

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The MEGA software package is the most comprehensive software I have used, if you don't want to rebuild your tree I have used FigTree in the past but it seems to be unsupported now.

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