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Anyone know good software for building cladograms?; Looking for certain specific requirements.
Topic Started: Nov 25 2017, 01:47 PM (329 Views)
SpeculativeNebula
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Fetus
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The only other topics I could find about this were years old so hoping something new has come about since then.

I have a project that I'm working on that I'd like to build a cladogram for. I'm hoping for a very simple visualisation of the relationships between species starting from abiogenesis. I have very specific requirements and I'm not expecting them all to be met, but I'd like to find the best solutiuon available.

This cladogram I'm drawing is going to get very large, easily exceeding 30,000 pixels in height once it's well underway. Because of this I would like to be able to collapse or visually isolate entire branches.

The ability to export to some kind of image file like PNG at full resolution without any obvious loss in quality is important - I want it to be sharable without viewers having to have a copy of the same program.

The cladogram is also continuously being updated and added to. This is why I would like a software that cleanly spaces the branches apart as they're being built upon.

Some potential candidates do not have the ability to decide the precise positioning of the points of divergence between the parent and two or more child nodes. I need it to be manual and not force snap to a position.

Adjustable timeline scale, or the ability to insert the scale as an image across the top.

I'm avoiding anything overly academic or focused on genetics - programs like MEGA are years of study beyond my understanding.

I'm looking for a software that allows a cladogram to be built from scratch, no need to upload a file.


This is what I've tried so far:

VUE WAS PERFECT - but the devs stopped updating it years ago and now importing to an image file like PNG or JPEG is broken. So I have a nice cladogram in there that I can't get out in any way. :( OR is only sharable to other people who have Vue. It does not export to PSD at a high enough resolution.

Photoshop - This is a viable but extremely cumbersome solution. It's not easy to continuously add to a tree in photoshop - you basically have to break the tree apart where you're adding it and rebuild it around the newly added data, sometimes having to increase the spacing between nodes all the way back to the abiogenesis (which means moving and reorientating every line that connects them). I've tried messing around with layers and things and there doesn't serem to be any easy way to do this. The other disadvantage of photoshop is that while collapsing branches is possible, it's again painstaking and breaks everything.

yEd graph editor - I don't know why but I just can't seem to get the hang of this. Ive been messing around with the program and trying to figure things out but it's so much less intuitive than other programs I've used. I tried just going ahead and making the tree, but I could not figure out how to get the internodes to branch.

Tree graph 2 was supposed to be buildable from scratch, but I never figured out how. It still seems to expect you to have a file to upload and create the tree from. Plus you can't insert images and it doesn't allow you to adjust the units on the distance scale - inches or centimetres only, can't change it to millions of years or any other measurement of time.

XMind - Was very limiting, no way to insert a timescale image and no adjustable scale of it's own. Nothing seemed collapsible.

MEGA - Too big and confusing for the simple job I want done. Definitely for academically-minded people, unlike me. I was interested at first because someone said you can make them from scratch, but I couldn't figure out how to even begin to use this program or what anything means.

Anyone else have any other ideas?
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Strychnos
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Hey! Hope this is useful, I haven't made a tree using a program for a while.

You might want to look into programs and/or sites that let you visualize a Newick string.

A Newick string is a relatively simple way of representing trees (compared to MEGA), but requires a little bit of practice to learn. I'm still not good at it, only used it to make trees for a few college projects.

Wikipedia links to Trex-online which seems like a decent way to generate trees with Newick strings, but seems to take a little while to respond.
I know there are better Newick viewers out there, but I'm having trouble finding them.

I hope this helps!


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SpeculativeNebula
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Thanks. I was hoping not to have to take that route but you're right it's probably the most viable solution. From what I can see it's not an insurmountable task to keep editing it and adding to it, as long as you know the language of the format. It would certainly open up options for programs with other features I need, plus there are programs that let you edit the tree in the UI if only you can get a starting Newick string file. Might just accept I have a bit to learn!
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Sceynyos-yos
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Every now and then users ask for this thing - wikipedia to the rescue: a generous list of PTVS.

I'm currently using treegraph 2 - it works, but it has its drawbacks. Phylodraw seems interesting as well.
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Strychnos
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Sceynyos-yos
Nov 27 2017, 03:43 PM
Every now and then users ask for this thing - wikipedia to the rescue: a generous list of PTVS.

I'm currently using treegraph 2 - it works, but it has its drawbacks. Phylodraw seems interesting as well.
Wow, nice! I had no idea that wikipedia had a list of software. I'll have to check some of these out!
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SpeculativeNebula
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Sceynyos-yos
Nov 27 2017, 03:43 PM
Every now and then users ask for this thing - wikipedia to the rescue: a generous list of PTVS.

I'm currently using treegraph 2 - it works, but it has its drawbacks. Phylodraw seems interesting as well.
And people still hate on Wikipedia... this is great! I never expected there to be a nice list anywhere like this. Thanks for linking to it!
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