Added phylogenetic code

mothur_otu.bat

@@ -82,3 +82,41 @@ cluster(column=final.dist, name=final.names)
 
 # Option 2: quick and dirty
 #cluster.split(fasta=final.fasta, taxonomy=final.taxonomy, name=final.names, taxlevel=3, processors=6)
+
+#The output from Option 2 should be about the same as Option 1. The remainder of this code uses Option 1
+
+#create a table that indicates the number of times an OTU shows up in each sample also known as a shared file
+#input: final.an.list and final.groups file
+#output: final.an.shared file
+make.shared(list=final.an.list, group=final.groups, label=0.03)
+
+#The final step to getting good OTU data is to normalize the number of sequences in each sample
+#First we need to know how many sequences are in each step
+count.groups()
+
+#sub-sample all the samples to the sample with the fewest sequences(4420)
+#input: final.an.shared file
+#output: final.an.unique.subsample.shared
+sub.sample(shared=final.an.shared, size=4420)
+
+#get the taxonomy information for each of our OTUs
+#DO NOT HAVE A TAXONOMY FILE
+#classify.otu(list=final.an.list, name=final.names, taxonomy=final.taxonomy, label=0.03)
+
+##Phylotype
+#goes through the taxonomy file and bins sequences together that have the same taxonomy
+#DO NOT HAVE A TAXONOMY FILE
+#phylotype(taxonomy=final.taxonomy, name=final.names, label=1)
+
+#make a shared file and standardize the number of sequences in each group
+make.shared(list=final.tx.list, group=final.groups, label=1)
+#DO NOT HAVE A TAXONOMY FILE
+#sub.sample(shared=final.tx.shared, size=4420)
+
+#get the taxonomy of each phylotype
+#DO NOT HAVE A TAXONOMY FILE
+#classify.otu(list=final.tx.list, name=final.names, taxonomy=final.taxonomy, label=1)
+
+##Phylogenetic tree
+#construct a phylip-formatted distance matrix
+dist.seqs(fasta=final.fasta, output=phylip, processors=2)