Quote:

---

Oreganic said:
Bravo! Nice microscopy/detective work St. Chibes!

---

Quote:

---

St. Chibes said:
Whoa Alan, my brain hurts from trying to figure out what those letters even mean! ahhah

What are those papers about? Something to do with DNA I take it?
Do you mind explaining or is it too in-depth to type out?

---

Quote:

---

Douglas Smith said:
Some steps for other beginners:

1. Go to GenBank, and search the Nucleotide database for what you
want. Save the search to a file, in "FASTA" format. Strip out
sequences that have "internal transcribed spacer" or "ITS".

2. Align the sequences with mafft:

http://mafft.cbrc.jp/alignment/software/

mafft --auto sequence.fasta > sequence_its2_align.fasta

3. Make the neighbor joining tree with ninja:

http://nimbletwist.com/software/ninja/download.html

./ninja_1.2.1/ninja sequence_its2_align.fasta > sequence_its2_nj.newick

4. View your nifty new tree with Archaeopteryx:

http://www.phylosoft.org/forester/download/forester.jar

And then choose and trim off the stuff that is more than 30% or so
different... and all the extra sequences... and do it all again.
And replace the GenBank numbers, with the names that you like in the
newick tree file.

And that is an easy way fast way to start making rough trees....

---

Quote:

---

Alan Rockefeller said:

Quote:

---

St. Chibes said:
Whoa Alan, my brain hurts from trying to figure out what those letters even mean! ahhah

What are those papers about? Something to do with DNA I take it?
Do you mind explaining or is it too in-depth to type out?

---

There are several sequences for Agrocybe erebia in genbank.  You can download the Agrocybe seqences and see how A. erebia fits into Agrocybe.  Knowing a bit about the phylogenetics will help you determine which microscopic and macroscopic features are relevant and increase your understanding of Agrocybe.

Quote:

---

Douglas Smith said:
Some steps for other beginners:

1. Go to GenBank, and search the Nucleotide database for what you
want. Save the search to a file, in "FASTA" format. Strip out
sequences that have "internal transcribed spacer" or "ITS".

2. Align the sequences with mafft:

http://mafft.cbrc.jp/alignment/software/

mafft --auto sequence.fasta > sequence_its2_align.fasta

3. Make the neighbor joining tree with ninja:

http://nimbletwist.com/software/ninja/download.html

./ninja_1.2.1/ninja sequence_its2_align.fasta > sequence_its2_nj.newick

4. View your nifty new tree with Archaeopteryx:

http://www.phylosoft.org/forester/download/forester.jar

And then choose and trim off the stuff that is more than 30% or so
different... and all the extra sequences... and do it all again.
And replace the GenBank numbers, with the names that you like in the
newick tree file.

And that is an easy way fast way to start making rough trees....

---

---

Thanks for posting this Alan,

but Sorry I'm such a dunce....
I've downloaded the software from the links and installed them.
....
and I'm completely lost after that....

How do you dowload the sequences?
How do you save the search in FASTA format?
How do you "strip" out the sequences that have "ITS"?

I'm using a Mac, if that makes a difference...