gene aliasing

[Guilherme Seger]

Dear Will Pearse.

Congratulations for this software! It is a great initiative!

My name is Guilherme Seger, I'm from Brazil. I'm doing my PhD at the phylogenetic and functional ecology lab./UFRGS.

I'm currently doing part of my PhD with Prof. Nathan Swenson at MSU.

I'm starting to work with pG and I'm with a problem at gene aliasing.

I want to make a tree using rbcl, ITS1 and trnL.

I wrote ITS1-internal_transcribed_spacer_1, but pG do not recognize it as two possible ways of writing the same marker (it gave me only zero results).

Can you please help me with it?

I think this way would be much more easier than downloading all sequences I need from genbank.

Best

Guilherme

[Will Pearse]

Hello,

Thanks for getting in touch; I'm glad you like the program!

Would it be possible for you to send me your species list (wdpe...@umn.edu) or just copy-paste a few of them in a reply below, since then I can figure out whether you not being able to find sequences is because the aliasing feature isn't working properly, or because there aren't any sequences for those species on GenBank.

In passing, a lot of users who've contacted me have found the Python interface to pG easier for building larger phylogenies with lots of aliases (I certainly do!); there's an example of this here (http://willpearse.github.io/phyloGenerator/scripting.html) on the site.

Cheers,

Will

[Will Pearse]

Hello,

After a little off-list discussion, there doesn't seem to be a problem with phyloGenerator not finding sequences it should be finding.

However, at the moment the online guide is not as helpful as it should be and I'm sorry for that. The gene aliasing is only available (at present) through the command line (e.g., when running "phyloGenerator.exe -gene rbcL-this_is_an_alias"), and not when using the program interactively. I'm patching that into the program now, and will release a minor update (v1.2a) with aliasing in the interactive prompt in the next few days.

Thanks again for your help Guilherme,

Will