Comments on Assignments #7:

Most of the Macs in the Maclab do not have enough memory to run the problem in assignment6 3B.

The two outfiles are here: without and with ASRV

> When I used treeview (version 1.6.1) to open testseq5.phy or

> testseq5b.phy which were got by using Clustalx, I can't open them

> on my PC, the screen shows "syntax error 715", could you tell what

> may cause that and how to solve it

The files ending on .phy are sequence alignments NOT tree files. The trees to use as a starting point were linked further down in the assignment. In general, if you cannot open a file, check it out in a text editor. In this case you used clustalx to transform the format of the alignment (from clustal format to phylip format) - you did not use it to create a tree.

> When I do the question3 (part A), you write "calculate branch

> lengths and likelihood values for the different trees", does that mean

> to change "computer clocklike branch lengths" (z) from No to Yes.

No, you don't want to assume a molecular clock, you just want to calculate branchlengths and their confidence intervals for a tree topology you enter.

> And I save the trees you gave to us as textfile (tree5b.txt) and delete

> ' in the textfile you mentioned, after that I run the Puzzle for

> question3, and "enter the file name for the user trees" tree5b.txt or

> test1.phy (one the tree I saved), but I can't get results from "outfile,

> outlm, outdist", I don't know why. How can I solve this problem?

On which machine are you running puzzle? If you do it under windows, you might want to start a DOS window, change to the PUZZLE directory using the DOS command “cd”, and start the program by typing puzzle. In windows, if you click on the puzzle icon, it runs in a DOS Window, but the window closes as soon as the program is finished. If the program finishes with an error message, you never see the message, because the window closes immediately after displaying the message. If you start Puzzle from within a DOS window, it stays open until you close it.

The reason you cannot open outfile might be there is nothing in it because the program aborted with an error (due to wrong format, or out of memory...). To solve this see above comment on windows. If the program finishes normally (it tells you in the window), you should be able to open the oufile with any text editor (notepad, word, simple text).

The outdist file also is a textfile (the same distance matrix is also displyed in outfile). The outml.eps file contains the output from the ml-mapping (i.e. it is only generated if you do ml mapping as in task#2. It has the same info as the outfile but as a much nicer graphic. You can open it with any program that reads postscript. I usually use Acrobat destiller (part of the acrobat package), but any number of graphics programs will do. - But you really can ignore this, as the same info is also in outfile.

When I use Dos to run puzzle, and after enter a file name for

user trees, if enter *.txt (for tree), the window shows "unable to

proceed (sequences missing in tree)"; if enter *.phy, the window

shows "there is ' in the file". I don't know what I should do then.

When asked for the sequences the file should be in phylip format (*.phy).

When asked for the usertree, the file should contain a text file with the tree in parenthesis notation. e.g., in case you want to address the question if the red algae group in a clade with the green algae the tree file containing two trees: would look like this:

2

(Giardia,(Trypanosom,Trichomona,Plasmodium,Entamoeba,((Dictyostel,((Nosema,(Schizosacc,(Neurospora,(Candida,(Eremotheci,Saccharomy))))),(Ascidia,(Homo1,Bos1,A1Gallus),(Manduca,Drosophila)))),(Cyanidium,((Scherffeli,(1Acetabula,2Acetabula)),(Beta,(Vigna,Gossypium,(Daucus,Brassica,Arabidopsi))))))));

(Giardia,(Trypanosom,Trichomona,Plasmodium,Entamoeba,(Cyanidium,(Dictyostel,((Nosema,(Schizosacc,(Neurospora,(Candida,(Eremotheci,Saccharomy))))),(Ascidia,(Homo1,Bos1,A1Gallus),(Manduca,Drosophila)))),((Scherffeli,(1Acetabula,2Acetabula)),(Beta,(Vigna,Gossypium,(Daucus,Brassica,Arabidopsi)))))));

However, the idea was for you to arrive at the two topologies yourself using the tree editor that is part of treeview. Again, you need to delete the ' if you copy and paste the trees from treeview into a text editor.

Of course, you need to make sure that the trees you supply, and the alignment you use, have the same names for the sequences. If , for example, in making the alignment file you left in some prokaryotic sequences, these are not part of the tree, and the program will tell you so. Could it be that you use testseq5 for the alignment, and a tree that corresponds to testseq5b.phy, i.e. a data set with many fewer species?