clstr_sqs: Identify clusters from sequences

In phylotaR: Automated Phylogenetic Sequence Cluster Identification from 'GenBank'

Description

Given a sequence object, this function will generate a list of cluster objects using BLAST

Usage

clstr_sqs(txid, sqs, ps, lvl, typ = c("direct", "subtree", "paraphyly"))

Arguments

txid	Taxonomic ID
sqs	Sequence object of sequences to be BLASTed
ps	Parameters list, generated with parameters()
lvl	Integer, number of message indentations indicating code depth.
typ	Direct, subtree or paraphyly?

See Also

Other run-private: batcher, blast_clstr, blast_filter, blast_setup, blast_sqs, blastcache_load, blastcache_save, blastdb_gen, blastn_run, cache_rm, cache_setup, clade_select, clstr2_calc, clstr_all, clstr_direct, clstr_subtree, clstrarc_gen, clstrarc_join, clstrrec_gen, clstrs_calc, clstrs_join, clstrs_merge, clstrs_renumber, clstrs_save, cmdln, descendants_get, download_obj_check, error, hierarchic_download, info, ncbicache_load, ncbicache_save, obj_check, obj_load, obj_save, parameters_load, parameters_setup, parent_get, progress_init, progress_read, progress_reset, progress_save, rank_get, safely_connect, search_and_cache, searchterm_gen, seeds_blast, seq_download, seqarc_gen, seqrec_augment, seqrec_convert, seqrec_gen, seqrec_get, sids_check, sids_get, sids_load, sids_save, sqs_count, sqs_load, sqs_save, stage_args_check, stages_run, tax_download, taxdict_gen, taxtree_gen, txids_get, txnds_count, warn

phylotaR documentation built on May 1, 2019, 9:26 p.m.