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I am trying to represent a large (100-300+ sequences) phylogenetic tree in a way that gets my point across. I figured that reducing the number of branches (by collapsing clades which include highly similar sequences) would be a good idea. The software that I'm currently using (iTOL) technically has an option for that ('collapse node'), but I'm not exactly a fan of the particular graphical representation, so I'd like to have a look at other options. Thank you for your time!

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    $\begingroup$ Try Figtree $\endgroup$ – NatWH May 21 at 16:13
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For Mac Figtree here is highly recommended, it is also available for Windows and Linux here. The technique is called "collapsing clades" and is the only package I know that does it. I would recommend using it, because I would assume it is averaging the branch length of a given clade and the 'base' of the triangle is proportional to the number of taxa. Thus it recognised as being very reliable, albeit the precise algorhithm it uses ... I don't know :-O

With FigTree you get two different "triangle options" in the menu, which give different shaped triangles for collapsing the number of lineages within the select clade you chose. The big one, is the algorhithm appropriately described above. It has many options for producing publication quality diagrams, albeit I then import the output into a graphics program for further editing (there are shortcomings IMO in colouring and fonts. Then again for free is better than good.

If you are outputing a tree within a script, ETE3 (Python) will do a "collapsing of clade" option, but it isn't pretty triangle stuff. ETE3 will produce a publication quality tree diagram from this and reduce to 'low resolution', which is very useful in large analyses of loads of trees.

In summary, I don't think FigTree has any competition in the context you are seeking.

Moreover, you can configure your bin, or alias file so you can automatically open a treefile just typing,

figtree treefile.tre

Also you can reduce you font size to next point 1 or 2 (okay you can do that in anything), if you are attempting optical analysis on loads of taxa. Its also really stable. I just find it really useful, like a "jazz standard" its a "phylogeny standard".

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