Man pages for phac-nml-phrsd/angedist
Antigenic Genetic Distance
| clean_seq_influenza_A | Clean influenza A sequences |
| clean_seq_influenza_B | Clean influenza B sequences |
| clean_strain_names_location_seq | Clean strain name. |
| dist_blosum | BLOSUM distance between two sequences. |
| dist_blosum_unit | Helper function for parallel computing. |
| dist_hamming | Hamming distance between two sequences. |
| dist_hamming_unit | Temporary function used in parallel computing of Hamming... |
| dist_matrix | Distance matrix for multiple sequences. |
| filter_index | Title |
| filter_location | Filter sequences based on the location name. |
| filter_seq_length | Filter sequences based on their length |
| filter_subseq | Filter sequences that have defined starting proteins. |
| get_accession_number | Retrieve the accession/ID number from the FASTA header. |
| get_collection_date | Get the collection date from a FASTA header. |
| import_seqs | Read and import genetic sequences from files. |
| locate_postion | Locate the most frequent starting position of sub-sequence... |
| mds | Multi-dimensional scaling |
| pathogen_code | Regex pathogen code in FASTA header. |
| pipe | Pipe operator |
| plot_mds | Plot a MDS object |
| remove_duplicated | Remove duplicated sequences. |
| remove_lowquality_seqs | Remove low-quality sequences. |
| subsample_date | Sub-sample sequences based on their collection date |
