remove_model_seqs: Remove Model Sequences
In jfq3/RDPutils: R Utilities for Processing RDPTool Output

Description Usage Arguments Details Value Author(s) Examples

This function removes model sequences from a combined fasta file.

1	remove_model_seqs(in_file, out_file = in_file)

`in_file`	The name of a combined fasta file with model sequences.
`out_file`	The name of the corresponding fasta file written to disk without model sequences.

This function operates on files. It is not normally assigned to a variable. By default, the input file is overwritten. If no model sequence is found in the input file, a message to that effect is returned.

RDP aligns 16S rRNA gene sequences using the Infernal aligner with model sequences for Bacteria or Archaea. A model sequence is introduced into each alignment. These model sequences are required by the cluster tool and the merge alignment tool. If a model sequence is present in the fasta file of representative sequences, it needs to be removed before the sequences can be treed with FastTree; this function provides the means to do so.

The function returns a message that it has completed.

John Quensen

1 2	in.file <- system.file("extdata", "all_seq_complete.clust_rep_seqs.fasta", package="RDPutils") remove_model_seqs(in_file=in.file, out_file = file2tree.fasta)