diff -r 729e90f1e874 -r 216bf44bf185 mothur/tools/suite_config.xml --- a/mothur/tools/suite_config.xml Mon Dec 03 09:09:43 2012 -0600 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,237 +0,0 @@ - - Calculate the number of potentially misaligned bases - - - Align sequences to a template alignment - - - Order Sequences by OTU - - - Generate a newick trees for dissimilarity among groups - - - Find putative chimeras using bellerophon - - - Find putative chimeras using ccode - - - Find putative chimeras using chimeraCheck - - - Find putative chimeras using pintail - - - Find putative chimeras using slayer - - - Trim sequences to a specified length - - - Assign sequences to taxonomy - - - Assign sequences to taxonomy - - - Generate a tree using relaxed neighbor joining - - - Assign sequences to OTUs (Dotur implementation) - - - Group sequences that are part of a larger sequence - - - Assign sequences to OTUs (Operational Taxonomic Unit) splits large matrices - - - Assign sequences to OTUs (Operational Taxonomic Unit) - - - Generate collector's curves for calculators on OTUs - - - Summary of calculator values for OTUs - - - Find a consensus sequence for each OTU or phylotype - - - correlation of data to axes - - - Remove gap characters from sequences - - - Return all sequences - - - calculate uncorrected pairwise distances between aligned sequences - - - Generate a phylip-formatted dissimilarity distance matrix among multiple groups - - - Convert fastq to fasta and quality - - - removes columns from alignments - - - Select groups - - - group names from shared or from list and group - - - Picks by taxon - - - Generate a fasta with a representative sequence for each OTU - - - Get otus containing sequences from specified groups - - - Calculate the relative abundance of each otu - - - Picks sequences by name - - - Assign sequences to OTUs (Operational Taxonomic Unit) - - - Generate a heatmap for OTUs - - - Generate a heatmap for pariwise similarity - - - Identify indicator "species" for nodes on a tree - - - Cramer-von Mises tests communities for the same structure - - - Lists the names of the sequences - - - Assign groups to Sets - - - Make a group file - - - Merge data - - - Merge groups in a shared file - - - generate principle components plot data - - - generate non-metric multidimensional scaling data - - - Normalize the number of sequences per group to a specified level - - - calculate uncorrected pairwise distances between sequences - - - Order Sequences by OTU - - - Describes whether two or more communities have the same structure - - - generate principle components plot data - - - Principal Coordinate Analysis - - - Alpha Diversity calculate unique branch length - - - Assign sequences to OTUs based on taxonomy - - - Remove sequences due to pyrosequencing errors - - - Generate inter-sample rarefaction curves for OTUs - - - Generate intra-sample rarefaction curves for OTUs - - - Read OTU list and group to create a shared file - - - Remove groups - - - Picks by taxon - - - Remove otus containing sequences from specified groups - - - Remove rare OTUs - - - Remove sequences by name - - - Reverse complement the sequences - - - Screen sequences - - - Summarize the quality of sequences - - - Separate sequences into rare and abundant groups - - - Generates a fasta file for each group - - - Create a sub sample - - - Summarize the quality of sequences - - - Summary of calculator values for OTUs - - - Summary of calculator values for OTUs - - - Generate a newick tree for dissimilarity among groups - - - Draw a Phylogenic Tree - - - Trim sequences - primers, barcodes, quality - - - Describes whether two or more communities have the same structure - - - Describes whether two or more communities have the same structure - - - Return unique sequences - - - Generate Venn diagrams gor groups -