Phylogenetic placement of short reads

Today I’ve been exploring how to place our short pyrosequencing reads into an evolutionary context.

RAxML EPA webserver ( )

  • Downloaded the SILVA 102 release non-redundant reference alignment, but ran into problems with guide tree uploading.  Apparently I need a tree with branch information AND alignment info, which I’m not sure how to do in ARB.  Have e-mailed Alexis and Simon Berger to see if they can help me prepare this file.

Placing sequences onto a tree in ARB

  • I’ve exported my ‘guide tree’ of nematode sequences from my thesis–file is saved as SSU_NematodeThesisRef_w99As_18Aug.arb on the IOMEGA data hard drive.  Full-length reference sequences are labelled as ‘Thesis Ref’ under the import field.  Nematode sequences from the 99A dataset are lablled as ‘Nema99A’ under the import field.