Files in phylotaR
Automated Phylogenetic Sequence Cluster Identification from 'GenBank'
MD5
LICENSE
DESCRIPTION
README.md
NAMESPACE
inst/doc/phylotaR.Rmd
inst/doc/phylotaR.R
inst/doc/phylotaR.html
vignettes/phylotaR.Rmd
R/tools-log.R
R/pipeline.R
R/tools-system.R
R/user-special.R
R/stage4-tools.R
R/tools-cache.R
R/stage3-tools.R
R/phylotaR.R
R/stage1.R
R/tools-entrez.R
R/stage1-tools.R
R/all-classes.R
R/user-calc.R
R/tools-sqs.R
R/stage4.R
R/pipeline-tools.R
R/stage3.R
R/tools-txdct.R
R/user-get.R
R/tools-tests.R
R/tools-blast.R
R/stage2.R
R/stage2-tools.R
R/tools-api.R
R/user-drop.R
man/tinamous.rd
man/warn.Rd
man/seqrec_gen.Rd
man/seqarc_gen.Rd
man/download_obj_check.Rd
man/tax_download.Rd
man/sids_load.Rd
man/get_ntaxa.Rd
man/cmdln.Rd
man/clstrrec_gen.Rd
man/blast_setup.Rd
man/sturgeons.rd
man/download_run.Rd
man/parameters_load.Rd
man/taxtree_gen.Rd
man/list_seqrec_slots.Rd
man/clstr_subtree.Rd
man/update_phylota.Rd
man/sqs_load.Rd
man/blast_clstr.Rd
man/clusters_run.Rd
man/progress_reset.Rd
man/cycads.rd
man/progress_read.Rd
man/ncbicache_save.Rd
man/drop_sqs.Rd
man/stage_args_check.Rd
man/get_tx_slot.Rd
man/searchterm_gen.Rd
man/plot_phylota_pa.Rd
man/txnds_count.Rd
man/ClstrArc-class.Rd
man/parameters.Rd
man/get_sq_slot.Rd
man/drop_by_rank.Rd
man/txids_get.Rd
man/ncbicache_load.Rd
man/clstr_sqs.Rd
man/rank_get.Rd
man/obj_check.Rd
man/tardigrades.rd
man/blastdb_gen.Rd
man/stages_run.Rd
man/ClstrRec-class.Rd
man/cache_setup.Rd
man/hierarchic_download.Rd
man/seqrec_augment.Rd
man/restart.Rd
man/seqrec_get.Rd
man/parent_get.Rd
man/obj_load.Rd
man/progress_save.Rd
man/clstrs_join.Rd
man/blast_sqs.Rd
man/calc_mad.Rd
man/clade_select.Rd
man/clstr2_calc.Rd
man/taxise_run.Rd
man/read_phylota.Rd
man/seq_download.Rd
man/sids_save.Rd
man/bromeliads.rd
man/clstrarc_gen.Rd
man/sqs_save.Rd
man/blastn_run.Rd
man/drop_clstrs.Rd
man/reset.Rd
man/sqs_count.Rd
man/SeqRec-class.Rd
man/is_txid_in_sq.Rd
man/batcher.Rd
man/get_clstr_slot.Rd
man/info.Rd
man/TaxRec-class.Rd
man/parameters_reset.Rd
man/error.Rd
man/clstrs_calc.Rd
man/clstr_direct.Rd
man/TaxDict-class.Rd
man/yeasts.rd
man/obj_save.Rd
man/progress_init.Rd
man/parameters_setup.Rd
man/seeds_blast.Rd
man/dragonflies.rd
man/aotus.rd
man/blast_filter.Rd
man/sids_check.Rd
man/sids_get.Rd
man/list_clstrrec_slots.Rd
man/list_taxrec_slots.Rd
man/descendants_get.Rd
man/get_nsqs.Rd
man/clstrs_renumber.Rd
man/blastcache_save.Rd
man/get_txids.Rd
man/run.Rd
man/safely_connect.Rd
man/clstrs_save.Rd
man/calc_wrdfrq.Rd
man/SeqArc-class.Rd
man/clstrs_merge.Rd
man/blastcache_load.Rd
man/clstr_all.Rd
man/is_txid_in_clstr.Rd
man/taxdict_gen.Rd
man/plot_phylota_treemap.Rd
man/write_sqs.Rd
man/cache_rm.Rd
man/mk_txid_in_sq_mtrx.Rd
man/clusters2_run.Rd
man/summary_phylota.Rd
man/Phylota-class.Rd
man/list_ncbi_ranks.Rd
man/search_and_cache.Rd
man/seqrec_convert.Rd
man/get_stage_times.Rd
man/setup.Rd
man/clstrarc_join.Rd
build/vignette.rds
tests/test-all.R
tests/testthat/test-stage3-tools.R
tests/testthat/test-stage4.R
tests/testthat/test-user-get.R
tests/testthat/test-user-calc.R
tests/testthat/test-tools-log.R
tests/testthat/test-tools-system.R
tests/testthat/test-stage3.R
tests/testthat/test-stage1-tools.R
tests/testthat/test-tools-sqs.R
tests/testthat/test-tools-txdct.R
tests/testthat/test-phylotar.R
tests/testthat/test-stage2-tools.R
tests/testthat/test-tools-entrez.R
tests/testthat/test-pipeline.R
tests/testthat/test-tools-cache.R
tests/testthat/test-stage1.R
tests/testthat/test-tools-pipeline.R
tests/testthat/test-tools-test.R
tests/testthat/test-stage2.R
tests/testthat/test-all-class.R
tests/testthat/test-user-drop.R
tests/testthat/test-user-special.R
tests/testthat/test-stage4-tools.R
tests/testthat/test-tools-api.R
tests/testthat/test-tools-blast.R
tests/testthat/data/raw_txrecs.rda
tests/testthat/data/clstrarc.rda
tests/testthat/data/sqrecs.rda
tests/testthat/data/raw_seqrecs.rda
tests/testthat/data/txdct.rda
tests/testthat/data/txrecs.rda
tests/testthat/data/taxonomy/txids_records.RData
tests/testthat/data/blast/README
tests/testthat/data/blast/testdb.nsq
tests/testthat/data/blast/blast_res.rda
tests/testthat/data/blast/testblstn
tests/testthat/data/blast/testdb.nin
tests/testthat/data/blast/testdb.nhr
tests/testthat/data/api/xml_timeout.rda
data/yeasts.rda
data/tardigrades.rda
data/aotus.rda
data/dragonflies.rda
data/cycads.rda
data/sturgeons.rda
data/datalist
data/tinamous.rda
data/bromeliads.rda
