Cladogram from STR Values

[jbarry6899]

I would appreciate your thoughts about the best method for drawing a cladogram from STR values.

I have a group of men who share a close 37 marker match and are divided between two surnames, X and Y. I would like to try to create a cladogram to make an educated guess about whether X descended from Y, Y from X or both from another common ancestor, Z.

I found instructions for creating cladograms using McGee's Y Utility at


Unfortunately this approach uses Fluxus which is available only for Windows, not for my Mac. I explored Phylip, which doesn't offer this function, and MacClade, which is no longer supported in Mac OS X. So I thought I would consult a bit before deciding whether to spend some $$ to partition my Mac to run Windows programs.

A few questions:

1. Are you aware of any other programs that will run on a Mac to create cladograms from STRs?

2. If not, do you have any ideas for creating cladograms manually? I have made spreadsheets to compare each of the results with the modal and minimum values, and partitioned the group into clusters based on shared mutations. But I'm not sure where to go from there in plotting the differences in a cladogram.

3. If drawing a diagram manually isn't feasible, would you draw any conclusions regarding the earlier surname on the basis of distance from the modal or minimum haplotypes? If so, which one would give the better insight?

Thanks!

Jim

[jbarry6899]

Cladogram from STR Values

I would appreciate your thoughts about the best method for drawing a cladogram from STR values.

I have a group of men who share a close 37 marker match and are divided between two surnames, X and Y. I would like to try to create a cladogram to make an educated guess about whether X descended from Y, Y from X or both from another common ancestor, Z.

I found instructions for creating cladograms using McGee's Y Utility at
http://lawsondna.org/results/cladograminstruction.html
Unfortunately this approach uses Fluxus which is available only for Windows, not for my Mac. I explored Phylip, which doesn't offer this function, and MacClade, which is no longer supported in Mac OS X. So I thought I would consult a bit before deciding whether to spend some $$ to partition my Mac to run Windows programs.

A few questions:

1. Are you aware of any other programs that will run on a Mac to create cladograms from STRs?

2. If not, do you have any ideas for creating cladograms manually? I have made spreadsheets to compare each of the results with the modal and minimum values, and partitioned the group into clusters based on shared mutations. But I'm not sure where to go from there in plotting the differences in a cladogram.

3. If drawing a diagram manually isn't feasible, would you draw any conclusions regarding the earlier surname on the basis of distance from the modal or minimum haplotypes? If so, which one would give the better insight?

Thanks!

Jim

[jbarry6899]

(Please excuse duplicate posting. Doesn't seem to be a way to delete.)

[KATM]

Did you check these out? I don't know if they will take STR values, but worth a try:

• http://Mesquite - http://mesquitepro...paces.com/home (10.6 & higher, to 10.10 Yosemite) - an alternative to MacClade, which will not work in OS X 10.7 and above
• Figtree (cross platform, Java program) http://tree.bio.ed.ac.uk/software/figtree/ - not sure if it works with latest OS X
• Dendroscope - have to get a license, but free (unclear if it works with latest OS X) http://dendroscope.org/

Perhaps one of them would work. I have no experience with any of them, or cladograms either, but did a search and found these.

[jbarry6899]

thanks; I will check them out.

[Kathy Johnston]

I would appreciate your thoughts about the best method for drawing a cladogram from STR values.

I have a group of men who share a close 37 marker match and are divided between two surnames, X and Y. I would like to try to create a cladogram to make an educated guess about whether X descended from Y, Y from X or both from another common ancestor, Z.

I found instructions for creating cladograms using McGee's Y Utility at


Unfortunately this approach uses Fluxus which is available only for Windows, not for my Mac. I explored Phylip, which doesn't offer this function, and MacClade, which is no longer supported in Mac OS X. So I thought I would consult a bit before deciding whether to spend some $$ to partition my Mac to run Windows programs.

A few questions:

1. Are you aware of any other programs that will run on a Mac to create cladograms from STRs?

2. If not, do you have any ideas for creating cladograms manually? I have made spreadsheets to compare each of the results with the modal and minimum values, and partitioned the group into clusters based on shared mutations. But I'm not sure where to go from there in plotting the differences in a cladogram.

3. If drawing a diagram manually isn't feasible, would you draw any conclusions regarding the earlier surname on the basis of distance from the modal or minimum haplotypes? If so, which one would give the better insight?

Thanks!

Jim

I think you will need to use a Microsoft program but I know there are some nice new features here:
http://www.crwarthen.com/downloads.htm

Charlie or his friend Wes can help you. Wes Erickson will be in the tent at Jamboree in Burbank this coming Friday morning (June 5) to discuss cladogram making if anybody lives in California. http://genealogyjamboree.com/2015/schedule-friday.html see JamboFREE World Roundtable Sessions.

[jbarry6899]

Thanks, Kathy--I think the Mesquite program posted earlier will work.

[royfarnol]

I would like to try making a cladogram to see what it might tell me so I downloaded Figtree.
Can someone please tell me what format of data the program requires and how to get it in that format from my Y results?

Thanks, Roy.

[jbarry6899]

I would like to try making a cladogram to see what it might tell me so I downloaded Figtree.
Can someone please tell me what format of data the program requires and how to get it in that format from my Y results?

Thanks, Roy.

Haven't tried Figtree. I decided to do it manually using this method:

http://www.johnbrobb.com/Content/DNA...usDiagrams.pdf

[royfarnol]

Fluxus & YSearch data questions

Is there a way to turn FTDNA's Y CSV results into a format Fluxus will handle - namely rdf, Fasta, Nexus or Phylip?

In my top ten YSearch matches I have 3 from an "other forensic DNA service". These folk have DNA results which are from a selection of markers that I got only with a 111 marker upgrade, I presume because they are believed to be less informative.

If this is true why would these "other" testers begin with less informative markers or is it that there are missing results on YSearch? Or is it something else?

[jbarry6899]

Is there a way to turn FTDNA's Y CSV results into a format Fluxus will handle - namely rdf, Fasta, Nexus or Phylip?

You might be able to use this method. I didn't try it because I found Mesquite, which is Mac compatible.

http://lawsondna.org/results/cladograminstruction.html

[royfarnol]

@jtbarry6899

Thanks. I've printed out that lot.
Roy.

[TWesley]

> Is there a way to turn FTDNA's Y CSV results into a format Fluxus will handle...

The Y-DNA utility written by Wes Erickson and Charlie Warthen:

link removed

...takes an .xml file (exported from FTDNA) and processes it so that it is compatible with the free "Network" phylogenetic software distributed by Fluxus Engineering.

The Y-DNA utility is a 32-bit Windows application which runs on Windows XP, Vista, 7, 8, and 10.

Our other utilities (ADNA and YSNP) are available for Windows and OSX (Macintosh).