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Fix link to newick format, closes #2122

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1 parent 3c23a00 commit 38e8a112190f54c524d431df0dc1a9b7382aab85 @colinbrislawn colinbrislawn committed Feb 2, 2016
Showing with 1 addition and 1 deletion.
  1. +1 −1 examples/ipynb/illumina_overview_tutorial.ipynb
@@ -232,7 +232,7 @@
"source": [
"The primary output that we get from this command is the *OTU table*, or the number of times each operational taxonomic unit (OTU) is observed in each sample. QIIME uses the Genomics Standards Consortium Biological Observation Matrix standard (BIOM) format for representing OTU tables. You can find additional information on the BIOM format [here](http://www.biom-format.org), and information on converting these files to tab-separated text that can be viewed in spreadsheet programs [here](http://biom-format.org/documentation/biom_conversion.html). Several OTU tables are generated by this command. The one we typically want to work with is ``otus/otu_table_mc2_w_tax_no_pynast_failures.biom``. This has singleton OTUs (or OTUs with a total count of 1) removed, as well as OTUs whose representative (i.e., centroid) sequence couldn't be aligned with [PyNAST](http://bioinformatics.oxfordjournals.org/content/26/2/266.long). It also contains taxonomic assignments for each OTU as *observation metadata*.\n",
"\n",
- "The open-reference OTU picking command also produces a phylogenetic tree where the tips are the OTUs. The file containing the tree is ``otus/rep_set.tre``, and is the file that should be used with ``otus/otu_table_mc2_w_tax_no_pynast_failures.biom`` in downstream phylogenetic diversity calculations. The tree is stored in the widely used [newick format](http://scikit-bio.org/docs/latest/generated/skbio.io.newick.html).\n",
+ "The open-reference OTU picking command also produces a phylogenetic tree where the tips are the OTUs. The file containing the tree is ``otus/rep_set.tre``, and is the file that should be used with ``otus/otu_table_mc2_w_tax_no_pynast_failures.biom`` in downstream phylogenetic diversity calculations. The tree is stored in the widely used [newick format](http://scikit-bio.org/docs/latest/generated/skbio.io.format.newick.html).\n",
"\n",
"To view the output of this command, call ``FileLink`` on the ``index.html`` file in the output directory."
]

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