Editing phylogenetics trees in FigTree

In this video I show you how you can edit and modify your phylogenetic tree using the program FigTree to make it nicer visually, easier to read, and more intuitive to understand. I use the same tree file as in my "Interpreting phylogenetics trees" video.
"Interpreting phylogenetics trees":
• Interpreting phylogene...
I post the link to the paper below, as well as a great article on colugos in WIRED. In case you would like to make the same tree I posted all files I used in my GitHub repository for you to download.
WIRED article on colugos:
www.wired.com/2014/11/absurd-...
Janecka et al. 2008 paper on cryptic diversity in colugos:
www.cell.com/current-biology/...
Files in GitHub repository:
github.com/janeckaj/sequence-...
ColugoMtDNA_information_on_alignment.docx (description of the sequence file)
ColugoMtDNAnoHSAv2.fas (sequence alignment)
ColugoMtDNAnoHSAv2.mtsx (MEGA tree session)
ColugoMtDNAnoHSAv2_ML_BS.nwk (tree in newick format)
ColugoMtDNAnoHSAv2_ML_BS.png (picture of tree)

[@viviannwokorogu7140]

Thank you so much for this video. I love how explicit your videos are, no more boring trees !!😂

[@cristianjaviermena6955]

Thanks Doc! from Cordoba, Argentina.

[@mirelapale2544]

I just loved it. you are amazing. Thank You

[@raniam.mahmoud9077]

Thanks a lot, it is very informative and helpful.

[@juliabarrauparraga2602]

It is a fantastic video. Thank you so much, you are a very good teacher. I learnt a lot.

[@vitoriaglenzel2021]

Thank you for this, it was very very helpful!!! :D

[@miaoyi1833]

Thank u a lot! It really helps a lot!!

[@ivanmateotamayoceballos7308]

Saludos desde Colombia. Muchas gracias por la información!!!

[@teengodees4040]

Has anyone had the problem that fig tree is suddenly not letting you export at all? I can see my trees and Edit them but I can’t export them. If anyone has any troubleshooting suggestions I would appreciate it.

[@user-pf3fi7xd7z]

On exporting or saving annotation on time slot 25:08 I see that you missed to check mark the annotation box which caused to make you think the Figtree dud not work although it did the second time you tried it. I have been trying to play with Figtree for more than 10 years and just found out this tutorial but I still learned new things on annotation, fish eye, exporting and powerpoint. I have also seen ggtree but is handy, although fig tree collapses some tree branches near zero ones which Mega can split it is still useful. I do not know why there is no tutorial about this.

[@rajeshkannan4932]

Thank you sir, Its very useful video sir for students sir, I have a one dout sir, In fig tree what indicates scale value ? how to write a result in discussion sir

[@aljanespinas503]

How to redo in fig tree?

[@amren2007]

Do you have any advice for saving larger trees with around 100 taxa in a way they are presentable and readable in a word document, when I stretch the PNG etc of my figtree in word it becomes unreadable and it’s really frustrating. The video was really helpful!

[@cat-et6dx]

Figtree is nice to visualize trees. For my dissertation I had to use a package in R. There are other ways using Python. I get frustrated too.

[@harry-pymdavis2482]

I've had a lot of success using [the free software] Inkscape! Export the file from FigTree as an SVG file then go to town!! What I like to do is fiddle with the tree as much as possible in FigTree first to make sure I don't accidentally mess with the branch lengths when it's an SVG file (these could just be my own unnecessary habits though). I like to expand it to a point where it's visually readable including branch/node values, and thicken the branches up a bit too. Then in Inkscape it's a case of jumping between locked and unlocked aspect ratios for the tree (you can ungroup the vector file if you want to colourise specific clades or shrink the root a bit for example), and editing the font of the labels and values until you're satisfied with it all. You can set the page size to A4, then when it comes to exporting the final product I export by "selection" or by "page" and that usually gives me a nice PNG to place in a Word manuscript. Good luck!! There are plenty of tutorials on KZbin for Inkscape too, so you'll be fine!! :)

[@user-pf3fi7xd7z]

I have also heard about Bluescape or something ArcGIS. I am going to see which one is free. Thanks that was something good!