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sheepslayer
10-07-2020, 03:40 PM
I want to make a tree like this:
40098


I want to do it manually by specifying branch lengths and placement. The only software I can find accepts tabular/sequence data to make these trees via clustering. I'm curious if anyone is aware of software that would allow me to do it manually

Dave-V
10-07-2020, 10:43 PM
First one that comes to mind is the Interactive Tree of Life. It still uses an uploaded file containing the branching specifications in various formats, but it allows for branch lengths to be specified and one of the output options is a normal rectilinear plot like you gave as example.

If you explore the help files and example input files here you can see if it meets your needs: https://itol.embl.de/upload.cgi

Otherwise for finer control over all the aspects you’d probably have to go to Powerpoint or another pure graphics package.

sheepslayer
10-08-2020, 03:54 PM
First one that comes to mind is the Interactive Tree of Life. It still uses an uploaded file containing the branching specifications in various formats, but it allows for branch lengths to be specified and one of the output options is a normal rectilinear plot like you gave as example.

If you explore the help files and example input files here you can see if it meets your needs: https://itol.embl.de/upload.cgi

Otherwise for finer control over all the aspects you’d probably have to go to Powerpoint or another pure graphics package.

I dig this but I might need to look to Powerpoint, in that I was just looking for something with a "Add Leaf" button that might spit out a Newick tree.. but this seems to rely on Newick input. It's all good and Newick isn't exactly rocket science either so I can manage. I appreciate you showing me this!

Dave-V
10-09-2020, 12:16 AM
If it helps, I have a generator that can produce portions of the haplotree (FTDNA version) in simple Newick format.

Here's one for all of Q-M242 as a TXT file: https://drive.google.com/file/d/1-41xk2ANoVZd1r8Iut6NkmB6ICNuPD0H/view?usp=sharing

It does not have branch lengths or any other specifiers in it besides just the raw tree, but hopefully it's a start.

I normally use it to produce simple tree pictures like this example for M242 (https://drive.google.com/file/d/1JSPrsbxL44T1uqt1rs4u_N7SMklqdN4i/view?usp=sharing), but they're automated and not configurable - hence the Newick output.

sheepslayer
10-09-2020, 01:01 AM
If it helps, I have a generator that can produce portions of the haplotree (FTDNA version) in simple Newick format.

Here's one for all of Q-M242 as a TXT file: https://drive.google.com/file/d/1-41xk2ANoVZd1r8Iut6NkmB6ICNuPD0H/view?usp=sharing

It does not have branch lengths or any other specifiers in it besides just the raw tree, but hopefully it's a start.

I normally use it to produce simple tree pictures like this example for M242 (https://drive.google.com/file/d/1JSPrsbxL44T1uqt1rs4u_N7SMklqdN4i/view?usp=sharing), but they're automated and not configurable - hence the Newick output.

I certainly appreciate it, I actually only chose the Q tree because it was the most aesthetically pleasing of Google's image results for "haplogroup dendrogram" :)

Your SNPTREE tool was indispensible to me for maintaining this spreadsheet I have of haplogroups in my family tree. I'm mostly R1b so I could just punch in 2 mutations and download the PNG with their common branch. Everything's in a tidy category now.

Anyway, would you happen to know of a way I could get Newick output from your tool, or whether you have this Newick machine on your site somewhere? Either way I'll trade you a tool for a tool: http://scaledinnovation.com/gg/adminUtils.html I asked the guy behind SNP Tracker if he could write something that can accept a mutation and return a tab-indented tree that I can copy and paste into XMind. I have yet to find something that will translate that into Newick, but I think I did a swell job typing up J-Z7671 by hand earlier today :)

Dave-V
10-09-2020, 01:08 AM
If you’ve used the SNPTREE tool before, just enter the SNP name as usual followed by a space and add the keyword NEWICK. The tool will produce a TXT file instead of the usual PNG file.

I do not have all haplogroups in the SNP database, but most or all of R and I should be there as well as J and Q.

sheepslayer
10-09-2020, 01:50 AM
If you’ve used the SNPTREE tool before, just enter the SNP name as usual followed by a space and add the keyword NEWICK. The tool will produce a TXT file instead of the usual PNG file.

I do not have all haplogroups in the SNP database, but most or all of R and I should be there as well as J and Q.

That's perfect, I appreciate it :)