Informatic Sequence Classification Trees
Allocate sequences for cross validation by identity.
Tree-based sequence classification.
Convert sequences between binary and character string formats.
Demultiplex merged FASTQ
Convert oligonucleotide sequences into regular expressions.
Encode and decode profile HMMs in raw byte format.
Expand an existing classification tree.
Get full lineage details from a taxonomic ID number.
Get taxon ID from taxonomy database.
Convert sequences to MD5 hashes.
Informatic sequence classification trees.
Concatenate DNAbin objects while preserving attributes.
Informatic sequence classification tree learning.
Further bit-level manipulation of DNA and amino acid sequences.
Prune taxonomy database.
Identify and remove erroneous reference sequences.
Quality filtering for amplicon sequences.
Reverse complement DNA in character string format.
Read FASTA and FASTQ files.
Dereplicate and rereplicate sequence datasets.
Query the NCBI GenBank database.
Shave ends from DNA and amino acid sequences
Paired-end read stitching.
Download taxonomy database.
Trim primer and/or index sequences.
Virtual in situ hybridization.
Virtual PCR.
Write sequences to text in FASTA or FASTQ format.
Provides tools for probabilistic taxon assignment with informatic sequence classification trees. See Wilkinson et al (2018) <doi:10.7287/peerj.preprints.26812v1>.
Useful links