Align.seqs removing most bp

[mww5124]

@westcott

What are the classifications of the 2 sequences from group 22A16 at node 26047? You should be able to open your tree file in a text editor and search for 26047 to find the names in the tree. Put those names in a accnos file and run:

get.seqs(names=yourNamesFile, group=yourGroupFile, taxonomy=yourTaxonomyFile, accnos=yourAccnosFile)
get.groups(name=current, group=current, taxonomy=current, group=22A16)

I ran those commands and got the following:

HMW292C01CFNA7 Bacteria(100);unclassified;unclassified;unclassified;unclassified;unclassified;
HMW292C01CFAKO Bacteria(100);unclassified;unclassified;unclassified;unclassified;unclassified;

[westcott]

Hmm… that doesn’t seem right. If you send your tree, taxonomy, name and groups files to mothur.bugs@gmail.com and I will try to get to the bottom of it.

[westcott]

Thanks for reporting this bug. I have found the issue and the fix will be part of our next release. It only effects the command when a names file is provided. So for the time being here’s a workaround:

deunique.seqs(fasta=yourFastaFile, name=yourNameFile) - make fasta file contain all seqs
classify.seqs(fasta=current) - get taxonomy file with all seqs
dist.seqs(fasta=current, output=lt) - distance matrix for clearcut with all seqs
clearcut(phylip=current) - get tree with all seqs
classify.tree(tree=current, taxonomy=current, group=yourGroupFile)