Gene listing in command line code

[Stefan Pinkert]

Hi Will,
thanks for this great tool your providing. A year ago I had to browse GenBank for hour just to check which sequences are already available ... now it needs a little bit of code and *pop* - there it is. To get this even more automated I use the command line, but I have problems with the inegration of several Genes. Seperating them with "," doesen't bring the expected result.

/Applications/phyloGeneratorMac/phyloGenerator.app/Contents/MacOS/phyloGenerator -name Odonata
-wd Applications/phyloGeneratorMac/Output -email Email -gene COI-cox1, COII-cox2, ND1, 12S, 16S, 18S, 28S, 5.6S .....

Thanks for your help.
Cheers, Stefan

[Will]

Hello,

Thanks for using the program Stefan, I'm glad it's helpful!

It looks like you might be separating them with a comma and a space, is that the case? If you are, then that should cause problems.

If that doesn't work, please do send me a copy of the output/error message and I'll figure it out.

Cheers,

Will

[Gustavo B Paterno]

Dear Will Pearse. First, thank you such much for this great tool!

I am having some problem to input my DNA data on phyloGenerator. I downaloded sequences for two genes of plant species (rbcl,matk) and saved the output like on the tutorial.

When I am runing the program again, and I want to use this sequences I can`t load my data, This is what I am doing:

/Users/Paterno/Desktop/Teste/Flower_Biomass_rbcl.fasta,/Users/Paterno/Desktop/Teste/Flower_Biomass_matk.fasta

File not found. Please try again!

But the files are there. If I input data for only one gene it reads well, so I think is something in my command.

I would apreciate any help,

Kind regards,

Gustavo

[Will]

Thanks for getting in touch, and thanks for using the program.

Make sure that:

• you're using the latest version of pG (i.e., you downloaded it within the last six months)
  
• the two files exist, and that their names are correct, by starting pG with both of the files separately (it sounds like you've done that)
• you've used the comma-separated entry with command line arguments to pG. So you're running it something like "phyloGenerator -existingAlignment first,second"

...if you've tried all those things, and it still doesn't work, send me a private email (wdpe...@umn.edu) with your operating system and the files and I'll take a look. There may be a problem with one/both of the files, although I can't think what!

Cheers,

Will

[Gustavo B Paterno]

Dear Will,

thank you very much for your support. I checked your recommendations and now it is working very well.

I now Have a second problem. PhyloGenartor do not accept my constrain tree. What is the best way to generate that?

I did my constrain tree in Phylomatic as suggested in the paper. From my species list, I got an newick tree with all my taxa. As I understood I need an unrooted tree so I did that on R since phylomatic output is rooted. 

However, when I try to use my constrain tree on phylogenerator it says that my species name do not match. But my species list was generated from the exactly same tree in R, after my check for speling errors inside R in species name.

Again, I would apreciate any help on that.

Kind regards,

Gustavo Paterno

[Will]

Hello,

I'm glad it seems to be working for you now.

I'm afraid this is a general "problem" with Phylomatic, not phyloGenerator; Phylomatic often makes files that are difficult for other programs to open (e.g., R's ape package; http://ape-package.ird.fr/ape_faq.html#phylomatic).

To narrow this down even more, your problem is likely coming from the tree not being compatible with the program RAxML, which is what phyloGenerator uses. Section 9 of the hands-on session (http://sco.h-its.org/exelixis/web/software/raxml/hands_on.html) gives a bit more detail about what a constraint tree should look like, but my general advice is to make sure there are no unecessary brackets in your tree (e.g., "(((A,B)),C);" is wrong, "((A,B),C);" is right). Make sure that the species in your DNA alignment are in your constraint tree and that they have the same capItaLisaTion.

Hopefully that helps. If you're really having trouble I could take a look for you, but every time I've taken a look it's always been one of the above things :D

Cheers,

Will