Cleanup of SSU tree in ARB

Today I started by cleaning up the tree a bit.  The Sourhope samples mostly didn’t add any information and just clogged up the tree, so I removed a total of 1922 unidentified Sourhope sequences from the tree–they are accessible in the ARB database, however..  They were marked with ‘sourhope removed’ in the import field.

The following groups were edited today:

  • Mesomermis
  • Monoposthia
  • Xiphinema
  • Pratylenchus
  • Phasmarhabditis
  • Strongyloides–the outlier sequences are a mess, although the main group is fine.  I removed species named ‘SgdRatt5’ and ‘RtdSpeci’ because they looked to be of bad quality.  They didn’t align coherently with fastaligner, and the sequences didn’t agree even the super-conserved regions.

I re-built the NJ tree at 9pm after today’s major edits–hopefully the groups will start falling into place.


Leave a Reply

Fill in your details below or click an icon to log in: Logo

You are commenting using your account. Log Out /  Change )

Google+ photo

You are commenting using your Google+ account. Log Out /  Change )

Twitter picture

You are commenting using your Twitter account. Log Out /  Change )

Facebook photo

You are commenting using your Facebook account. Log Out /  Change )


Connecting to %s

%d bloggers like this: