Files in pmgrollemund/phyloHIV
.Rbuildignore
.gitignore
DESCRIPTION
Meta/vignette.rds
NAMESPACE
R/align_related_functions.R
R/building_tree_functions.R
R/clades_related_functions.R
R/other_functions.R
README.md
doc/phyloHIV_Example.R
doc/phyloHIV_Example.Rmd
doc/phyloHIV_Example.html
doc/phyloHIV_options.R
doc/phyloHIV_options.Rmd
doc/phyloHIV_options.html
doc/phyloHIV_vignette.R
doc/phyloHIV_vignette.Rmd
doc/phyloHIV_vignette.html
inst/ext/fasta-splitter.pl
inst/ext/phyloscanner_analyse_trees.R
inst/extdata/Align/Closest_result.rda
inst/extdata/Align/LANL_Subtype_01_AE_closest.fasta
inst/extdata/Align/LANL_Subtype_01_AE_match.txt
inst/extdata/Align/LANL_Subtype_A1_closest.fasta
inst/extdata/Align/LANL_Subtype_A1_match.txt
inst/extdata/Align/indexes_identical.rda
inst/extdata/Align/newseq_LANL_Subtype_01_AE.fasta
inst/extdata/Align/newseq_LANL_Subtype_01_AE_mafft_aligned.fasta
inst/extdata/Align/newseq_LANL_Subtype_01_AE_mafft_aligned_ndrm.fasta
inst/extdata/Align/newseq_LANL_Subtype_A1.fasta
inst/extdata/Align/newseq_LANL_Subtype_A1_mafft_aligned.fasta
inst/extdata/Align/newseq_LANL_Subtype_A1_mafft_aligned_ndrm.fasta
inst/extdata/Align/outgroup.rda
inst/extdata/Clades/Clades_save.RData
inst/extdata/Clades/Clades_save_000.RData
inst/extdata/Clades/Clades_save_001.RData
inst/extdata/Colored_tree/newseq_LANL_Subtype_01_AE_mafft_aligned_ndrm_rerooted_renamed/newseq_LANL_Subtype_01_AE_mafft_aligned_ndrm_ft.000_rerooted_renamed.newick_processedTree.pdf
inst/extdata/Colored_tree/newseq_LANL_Subtype_01_AE_mafft_aligned_ndrm_rerooted_renamed/newseq_LANL_Subtype_01_AE_mafft_aligned_ndrm_ft.000_rerooted_renamed.newick_workspace.rda
inst/extdata/Colored_tree/newseq_LANL_Subtype_01_AE_mafft_aligned_ndrm_rerooted_renamed/newseq_LANL_Subtype_01_AE_mafft_aligned_ndrm_ft.000_rerooted_renamed_MRCA.txt
inst/extdata/Colored_tree/newseq_LANL_Subtype_01_AE_mafft_aligned_ndrm_rerooted_renamed/newseq_LANL_Subtype_01_AE_mafft_aligned_ndrm_ft.000_rerooted_renamed_trait.csv
inst/extdata/Colored_tree/newseq_LANL_Subtype_01_AE_mafft_aligned_ndrm_rerooted_renamed/newseq_LANL_Subtype_01_AE_mafft_aligned_ndrm_ft.001_rerooted_renamed.newick_processedTree.pdf
inst/extdata/Colored_tree/newseq_LANL_Subtype_01_AE_mafft_aligned_ndrm_rerooted_renamed/newseq_LANL_Subtype_01_AE_mafft_aligned_ndrm_ft.001_rerooted_renamed.newick_workspace.rda
inst/extdata/Colored_tree/newseq_LANL_Subtype_01_AE_mafft_aligned_ndrm_rerooted_renamed/newseq_LANL_Subtype_01_AE_mafft_aligned_ndrm_ft.001_rerooted_renamed_MRCA.txt
inst/extdata/Colored_tree/newseq_LANL_Subtype_01_AE_mafft_aligned_ndrm_rerooted_renamed/newseq_LANL_Subtype_01_AE_mafft_aligned_ndrm_ft.001_rerooted_renamed_trait.csv
inst/extdata/Colored_tree/newseq_LANL_Subtype_01_AE_mafft_aligned_ndrm_rerooted_renamed/newseq_LANL_Subtype_01_AE_mafft_aligned_ndrm_rerooted_renamed.newick_processedTree.pdf
inst/extdata/Colored_tree/newseq_LANL_Subtype_01_AE_mafft_aligned_ndrm_rerooted_renamed/newseq_LANL_Subtype_01_AE_mafft_aligned_ndrm_rerooted_renamed.newick_workspace.rda
inst/extdata/Colored_tree/newseq_LANL_Subtype_01_AE_mafft_aligned_ndrm_rerooted_renamed/newseq_LANL_Subtype_01_AE_mafft_aligned_ndrm_rerooted_renamed_MRCA.txt
inst/extdata/Colored_tree/newseq_LANL_Subtype_01_AE_mafft_aligned_ndrm_rerooted_renamed/newseq_LANL_Subtype_01_AE_mafft_aligned_ndrm_rerooted_renamed_trait.csv
inst/extdata/Colored_tree/newseq_LANL_Subtype_A1_mafft_aligned_ndrm_rerooted_renamed/newseq_LANL_Subtype_A1_mafft_aligned_ndrm_ft.000_rerooted_renamed.newick_processedTree.pdf
inst/extdata/Colored_tree/newseq_LANL_Subtype_A1_mafft_aligned_ndrm_rerooted_renamed/newseq_LANL_Subtype_A1_mafft_aligned_ndrm_ft.000_rerooted_renamed.newick_workspace.rda
inst/extdata/Colored_tree/newseq_LANL_Subtype_A1_mafft_aligned_ndrm_rerooted_renamed/newseq_LANL_Subtype_A1_mafft_aligned_ndrm_ft.000_rerooted_renamed_MRCA.txt
inst/extdata/Colored_tree/newseq_LANL_Subtype_A1_mafft_aligned_ndrm_rerooted_renamed/newseq_LANL_Subtype_A1_mafft_aligned_ndrm_ft.000_rerooted_renamed_trait.csv
inst/extdata/Colored_tree/newseq_LANL_Subtype_A1_mafft_aligned_ndrm_rerooted_renamed/newseq_LANL_Subtype_A1_mafft_aligned_ndrm_ft.001_rerooted_renamed.newick_processedTree.pdf
inst/extdata/Colored_tree/newseq_LANL_Subtype_A1_mafft_aligned_ndrm_rerooted_renamed/newseq_LANL_Subtype_A1_mafft_aligned_ndrm_ft.001_rerooted_renamed.newick_workspace.rda
inst/extdata/Colored_tree/newseq_LANL_Subtype_A1_mafft_aligned_ndrm_rerooted_renamed/newseq_LANL_Subtype_A1_mafft_aligned_ndrm_ft.001_rerooted_renamed_MRCA.txt
inst/extdata/Colored_tree/newseq_LANL_Subtype_A1_mafft_aligned_ndrm_rerooted_renamed/newseq_LANL_Subtype_A1_mafft_aligned_ndrm_ft.001_rerooted_renamed_trait.csv
inst/extdata/Colored_tree/newseq_LANL_Subtype_A1_mafft_aligned_ndrm_rerooted_renamed/newseq_LANL_Subtype_A1_mafft_aligned_ndrm_rerooted_renamed.newick_processedTree.pdf
inst/extdata/Colored_tree/newseq_LANL_Subtype_A1_mafft_aligned_ndrm_rerooted_renamed/newseq_LANL_Subtype_A1_mafft_aligned_ndrm_rerooted_renamed.newick_workspace.rda
inst/extdata/Colored_tree/newseq_LANL_Subtype_A1_mafft_aligned_ndrm_rerooted_renamed/newseq_LANL_Subtype_A1_mafft_aligned_ndrm_rerooted_renamed_MRCA.txt
inst/extdata/Colored_tree/newseq_LANL_Subtype_A1_mafft_aligned_ndrm_rerooted_renamed/newseq_LANL_Subtype_A1_mafft_aligned_ndrm_rerooted_renamed_trait.csv
inst/extdata/FakeData/Country_db.rds
inst/extdata/FakeData/person_modified.rds
inst/extdata/FakeData/sequences_meta_modified.rds
inst/extdata/LANL/HXB2.fasta
inst/extdata/LANL/LANL_Subtype_01_AE.db.nhr
inst/extdata/LANL/LANL_Subtype_01_AE.db.nin
inst/extdata/LANL/LANL_Subtype_01_AE.db.nsq
inst/extdata/LANL/LANL_Subtype_01_AE.fasta
inst/extdata/LANL/LANL_Subtype_01_AE_closest.txt
inst/extdata/LANL/LANL_Subtype_A1.db.nhr
inst/extdata/LANL/LANL_Subtype_A1.db.nin
inst/extdata/LANL/LANL_Subtype_A1.db.nsq
inst/extdata/LANL/LANL_Subtype_A1.fasta
inst/extdata/LANL/LANL_Subtype_A1_closest.txt
inst/extdata/Local/newseq_Subtype_01_AE.fasta
inst/extdata/Local/newseq_Subtype_A1.fasta
inst/extdata/Manual_alignment/Manual_alignment_123_after.png
inst/extdata/Manual_alignment/Manual_alignment_123_before.png
inst/extdata/Manual_alignment/Manual_alignment_19_after.png
inst/extdata/Manual_alignment/Manual_alignment_19_before.png
inst/extdata/Manual_alignment/Manual_alignment_83_after.png
inst/extdata/Manual_alignment/Manual_alignment_83_before.png
inst/extdata/Tree/fasttree_newseq_LANL_Subtype_01_AE_mafft_aligned_ndrm/Blacklist_newseq_LANL_Subtype_01_AE_mafft_aligned_ndrm_ft.000_rerooted_renamed.txt
inst/extdata/Tree/fasttree_newseq_LANL_Subtype_01_AE_mafft_aligned_ndrm/Blacklist_newseq_LANL_Subtype_01_AE_mafft_aligned_ndrm_ft.001_rerooted_renamed.txt
inst/extdata/Tree/fasttree_newseq_LANL_Subtype_01_AE_mafft_aligned_ndrm/Blacklist_newseq_LANL_Subtype_01_AE_mafft_aligned_ndrm_rerooted_renamed.txt
inst/extdata/Tree/fasttree_newseq_LANL_Subtype_01_AE_mafft_aligned_ndrm/RAxML_bipartitionsBranchLabels.newseq_LANL_Subtype_01_AE_mafft_aligned_ndrm.newick
inst/extdata/Tree/fasttree_newseq_LANL_Subtype_01_AE_mafft_aligned_ndrm/RAxML_info.newseq_LANL_Subtype_01_AE_mafft_aligned_ndrm.newick
inst/extdata/Tree/fasttree_newseq_LANL_Subtype_01_AE_mafft_aligned_ndrm/newseq_LANL_Subtype_01_AE_mafft_aligned_ndrm.newick
inst/extdata/Tree/fasttree_newseq_LANL_Subtype_01_AE_mafft_aligned_ndrm/newseq_LANL_Subtype_01_AE_mafft_aligned_ndrm_ft.000.newick
inst/extdata/Tree/fasttree_newseq_LANL_Subtype_01_AE_mafft_aligned_ndrm/newseq_LANL_Subtype_01_AE_mafft_aligned_ndrm_ft.000.newick.log
inst/extdata/Tree/fasttree_newseq_LANL_Subtype_01_AE_mafft_aligned_ndrm/newseq_LANL_Subtype_01_AE_mafft_aligned_ndrm_ft.000_rerooted.newick
inst/extdata/Tree/fasttree_newseq_LANL_Subtype_01_AE_mafft_aligned_ndrm/newseq_LANL_Subtype_01_AE_mafft_aligned_ndrm_ft.000_rerooted_renamed.newick
inst/extdata/Tree/fasttree_newseq_LANL_Subtype_01_AE_mafft_aligned_ndrm/newseq_LANL_Subtype_01_AE_mafft_aligned_ndrm_ft.001.newick
inst/extdata/Tree/fasttree_newseq_LANL_Subtype_01_AE_mafft_aligned_ndrm/newseq_LANL_Subtype_01_AE_mafft_aligned_ndrm_ft.001.newick.log
inst/extdata/Tree/fasttree_newseq_LANL_Subtype_01_AE_mafft_aligned_ndrm/newseq_LANL_Subtype_01_AE_mafft_aligned_ndrm_ft.001_rerooted.newick
inst/extdata/Tree/fasttree_newseq_LANL_Subtype_01_AE_mafft_aligned_ndrm/newseq_LANL_Subtype_01_AE_mafft_aligned_ndrm_ft.001_rerooted_renamed.newick
inst/extdata/Tree/fasttree_newseq_LANL_Subtype_01_AE_mafft_aligned_ndrm/newseq_LANL_Subtype_01_AE_mafft_aligned_ndrm_rerooted.newick
inst/extdata/Tree/fasttree_newseq_LANL_Subtype_01_AE_mafft_aligned_ndrm/newseq_LANL_Subtype_01_AE_mafft_aligned_ndrm_rerooted_renamed.newick
inst/extdata/Tree/fasttree_newseq_LANL_Subtype_A1_mafft_aligned_ndrm/Blacklist_newseq_LANL_Subtype_A1_mafft_aligned_ndrm_ft.000_rerooted_renamed.txt
inst/extdata/Tree/fasttree_newseq_LANL_Subtype_A1_mafft_aligned_ndrm/Blacklist_newseq_LANL_Subtype_A1_mafft_aligned_ndrm_ft.001_rerooted_renamed.txt
inst/extdata/Tree/fasttree_newseq_LANL_Subtype_A1_mafft_aligned_ndrm/Blacklist_newseq_LANL_Subtype_A1_mafft_aligned_ndrm_rerooted_renamed.txt
inst/extdata/Tree/fasttree_newseq_LANL_Subtype_A1_mafft_aligned_ndrm/RAxML_bipartitionsBranchLabels.newseq_LANL_Subtype_A1_mafft_aligned_ndrm.newick
inst/extdata/Tree/fasttree_newseq_LANL_Subtype_A1_mafft_aligned_ndrm/RAxML_info.newseq_LANL_Subtype_A1_mafft_aligned_ndrm.newick
inst/extdata/Tree/fasttree_newseq_LANL_Subtype_A1_mafft_aligned_ndrm/newseq_LANL_Subtype_A1_mafft_aligned_ndrm.newick
inst/extdata/Tree/fasttree_newseq_LANL_Subtype_A1_mafft_aligned_ndrm/newseq_LANL_Subtype_A1_mafft_aligned_ndrm_ft.000.newick
inst/extdata/Tree/fasttree_newseq_LANL_Subtype_A1_mafft_aligned_ndrm/newseq_LANL_Subtype_A1_mafft_aligned_ndrm_ft.000.newick.log
inst/extdata/Tree/fasttree_newseq_LANL_Subtype_A1_mafft_aligned_ndrm/newseq_LANL_Subtype_A1_mafft_aligned_ndrm_ft.000_rerooted.newick
inst/extdata/Tree/fasttree_newseq_LANL_Subtype_A1_mafft_aligned_ndrm/newseq_LANL_Subtype_A1_mafft_aligned_ndrm_ft.000_rerooted_renamed.newick
inst/extdata/Tree/fasttree_newseq_LANL_Subtype_A1_mafft_aligned_ndrm/newseq_LANL_Subtype_A1_mafft_aligned_ndrm_ft.001.newick
inst/extdata/Tree/fasttree_newseq_LANL_Subtype_A1_mafft_aligned_ndrm/newseq_LANL_Subtype_A1_mafft_aligned_ndrm_ft.001.newick.log
inst/extdata/Tree/fasttree_newseq_LANL_Subtype_A1_mafft_aligned_ndrm/newseq_LANL_Subtype_A1_mafft_aligned_ndrm_ft.001_rerooted.newick
inst/extdata/Tree/fasttree_newseq_LANL_Subtype_A1_mafft_aligned_ndrm/newseq_LANL_Subtype_A1_mafft_aligned_ndrm_ft.001_rerooted_renamed.newick
inst/extdata/Tree/fasttree_newseq_LANL_Subtype_A1_mafft_aligned_ndrm/newseq_LANL_Subtype_A1_mafft_aligned_ndrm_rerooted.newick
inst/extdata/Tree/fasttree_newseq_LANL_Subtype_A1_mafft_aligned_ndrm/newseq_LANL_Subtype_A1_mafft_aligned_ndrm_rerooted_renamed.newick
inst/extdata/before_running/FakeData/Country_db.rds
inst/extdata/before_running/FakeData/person_modified.rds
inst/extdata/before_running/FakeData/sequences_meta_modified.rds
inst/extdata/before_running/LANL/HXB2.fasta
inst/extdata/before_running/LANL/LANL_Subtype_01_AE.fasta
inst/extdata/before_running/LANL/LANL_Subtype_A1.fasta
inst/extdata/before_running/Local/newseq_Subtype_01_AE.fasta
inst/extdata/before_running/Local/newseq_Subtype_A1.fasta
inst/extdata/nucl_div.rda
inst/extjson/internal_options.json
inst/extjson/options.json
inst/extpreprocess/options_preprocess.json
inst/extpreprocess/preprocess_LANL.R
inst/extpreprocess/preprocess_rds_file.R
inst/extscript/Ancestral_state_to_clades.R
inst/extscript/align_sequences.R
inst/extscript/build_trees.R
man/MRCA_correction.Rd
man/add_outgroup.Rd
man/align_seq.Rd
man/blastn.Rd
man/building_tree.Rd
man/check_HXB2.Rd
man/clades_extracting.Rd
man/clean_LANL.Rd
man/extract_HXB2.Rd
man/find_identical_sequences.Rd
man/get_closest_seq.Rd
man/is.unique.Rd
man/makeblastdb.Rd
man/phyloscanner_postprocess.Rd
man/postprocess_tree.Rd
man/rm_DRM.Rd
man/rm_gaps_LANL.Rd
man/seq_rm_drugresistance2.Rd
man/tips_relabelling.Rd
man/tips_relabelling.internal.Rd
man/wrap_extract.clades.Rd
man/wrap_phyloscanner_analyse_tree.Rd
man/write_option_file.Rd
man/write_qsub.Rd
phyloHIV.Rproj
phyloHIV_0.1.0.tar.gz
vignettes/.gitignore
vignettes/phyloHIV_Example.Rmd
vignettes/phyloHIV_options.Rmd
vignettes/phyloHIV_vignette.Rmd
