McTavishLab/physcraperex
Physcraper Workflow Examples

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Physcraper Workflow Examples

.Rbuildignore
.gitignore
DESCRIPTION
NAMESPACE
R/plots.R R/tip_labels.R README.md
_pkgdown.yml
data-raw/DATASET.R
data-raw/alignments/T1281-M2478.nex
data-raw/alignments/T6859-M4727.nex
data-raw/alignments/TB2:Tr240.nex
data-raw/alignments/Tr5276-M3802-mod.nex
data-raw/alignments/Tr5276-M3802.nex
data-raw/alignments/Tr5276-M3938-mod.nex
data-raw/alignments/Tr5276-M3938.nex
data-raw/alignments/Tr5276-M3939-mod.nex
data-raw/alignments/Tr5276-M3939.nex
data-raw/alignments/Tr5276-M3956-mod.nex
data-raw/alignments/Tr5276-M3956.nex
data-raw/densitree-plots.Rmd
data-raw/ilex-images/cotree-plot1-1.png
data-raw/ilex-images/cotree-plot2-1.png
data-raw/ilex-images/cotree-plot3-1.png
data-raw/ilex-images/newer-tree-1.png
data-raw/ilex-images/original-tree-1.png
data-raw/ilex-images/updated-tree-otus-1.png
data-raw/ilex-images/updated-tree-taxonname-1.png
data-raw/ilex-test/alignment_T1281_M2478_pruned.nex
data-raw/ilex-test/ilex-test-local-run-2021-02-23.txt
data-raw/ilex-test/ilex-test-local-run.txt
data-raw/ilex-test/pruned_tree_tip_labels.txt
data-raw/ilex-test/pruned_tree_tip_labels_mapped/main.json
data-raw/ilex-test/pruned_tree_tip_labels_mapped/output/main.csv
data-raw/ilex-test/pruned_tree_tip_labels_mapped/output/main.tsv
data-raw/ilex-test/tree6577_pg_2827_pruned.nex
data-raw/ilex-test/tree6577_pg_2827_pruned.tre
data-raw/jobs/ilex_2020.06.28-1.sub
data-raw/jobs/ilex_2020.06.28-2.sub
data-raw/jobs/ilex_2020.06.28_1545015.stdout
data-raw/jobs/ilex_2020.06.28_1545016.stdout
data-raw/jobs/schoch_ascomycota_1_2020.06.06.sub
data-raw/jobs/schoch_ascomycota_2_2020.06.06.sub
data-raw/jobs/schoch_ascomycota_3_2020.06.06.sub
data-raw/jobs/schoch_ascomycota_4_2020.06.06.sub
data-raw/malvaceae-images/cotree-plot1-1.png
data-raw/malvaceae-images/cotree-plot2-1.png
data-raw/malvaceae-images/get-tree-1.png
data-raw/malvaceae-images/simmap-1.png
data-raw/malvaceae-images/simmap-2.png
data-raw/malvaceae-images/simmap-plot-1.png
data-raw/malvaceae-images/simmap-plot-2.png
data-raw/malvaceae-images/unnamed-chunk-10-1.png
data-raw/malvaceae-images/unnamed-chunk-7-1.png
data-raw/plots-treebase.Rmd data-raw/studies/cavender2006phylogenetic.pdf data-raw/studies/cuenoud2000molecular.pdf data-raw/studies/manen2010complex.pdf data-raw/studies/park2019complete.pdf data-raw/studies/selbach2009new.pdf data-raw/studies/setoguchi2000intersectional.pdf data-raw/trees/treebase/S1091-pdf/T1266.pdf data-raw/trees/treebase/S1091-pdf/T1267.pdf data-raw/trees/treebase/S1091-pdf/T1268.pdf data-raw/trees/treebase/S1091-pdf/T1269.pdf data-raw/trees/treebase/S1091-pdf/T1270.pdf data-raw/trees/treebase/S1091-pdf/T1271.pdf data-raw/trees/treebase/S1091-pdf/T1272.pdf data-raw/trees/treebase/S1091-pdf/T1273.pdf data-raw/trees/treebase/S1091-pdf/T1274.pdf data-raw/trees/treebase/S1091-pdf/T1275.pdf data-raw/trees/treebase/S1091-pdf/T1276.pdf data-raw/trees/treebase/S1091-pdf/T1277.pdf data-raw/trees/treebase/S1091-pdf/T1278.pdf data-raw/trees/treebase/S1091-pdf/T1279.pdf data-raw/trees/treebase/S1091-pdf/T1280.pdf data-raw/trees/treebase/S1091-pdf/T1281.pdf
data-raw/trees/treebase/S1091-treefiles.csv
data-raw/trees/treebase/S1091/T1266.nex
data-raw/trees/treebase/S1091/T1267.nex
data-raw/trees/treebase/S1091/T1268.nex
data-raw/trees/treebase/S1091/T1269.nex
data-raw/trees/treebase/S1091/T1270.nex
data-raw/trees/treebase/S1091/T1271.nex
data-raw/trees/treebase/S1091/T1272.nex
data-raw/trees/treebase/S1091/T1273.nex
data-raw/trees/treebase/S1091/T1274.nex
data-raw/trees/treebase/S1091/T1275.nex
data-raw/trees/treebase/S1091/T1276.nex
data-raw/trees/treebase/S1091/T1277.nex
data-raw/trees/treebase/S1091/T1278.nex
data-raw/trees/treebase/S1091/T1279.nex
data-raw/trees/treebase/S1091/T1280.nex
data-raw/trees/treebase/S1091/T1281.nex
data-raw/trees/treebase/S2137/Tr5276.nex
data-raw/trees/treebase/S2137/Tr5277.nex
data/ilex-local/inputs_T1281-M2478/mrca.txt
data/ilex-local/inputs_T1281-M2478/otu_info_T1281-M2478.csv
data/ilex-local/inputs_T1281-M2478/physcraper_T1281-M2478.fas
data/ilex-local/inputs_T1281-M2478/physcraper_T1281-M2478.tre
data/ilex-local/inputs_T1281-M2478/taxonname.fas
data/ilex-local/inputs_T1281-M2478/taxonname.tre
data/ilex-local/labelled_T1281-M2478.fas
data/ilex-local/labelled_T1281-M2478.tre
data/ilex-local/outputs_T1281-M2478/otu_info_T1281-M2478.csv
data/ilex-local/outputs_T1281-M2478/physcraper_T1281-M2478.fas
data/ilex-local/outputs_T1281-M2478/physcraper_T1281-M2478.tre
data/ilex-local/outputs_T1281-M2478/updated_taxonname.fas
data/ilex-local/outputs_T1281-M2478/updated_taxonname.tre
data/ilex-local/run_T1281-M2478/RAxML_bestTree.2020-06-29
data/ilex-local/run_T1281-M2478/RAxML_bootstrap.BOOT2020-06-29
data/ilex-local/run_T1281-M2478/RAxML_info.2020-06-29
data/ilex-local/run_T1281-M2478/RAxML_info.BOOT2020-06-29
data/ilex-local/run_T1281-M2478/RAxML_log.2020-06-29
data/ilex-local/run_T1281-M2478/RAxML_result.2020-06-29
data/ilex-local/run_T1281-M2478/all_align_T1281-M2478.fas
data/ilex-local/run_T1281-M2478/blast_run_T1281-M2478/otu420067.txt
data/ilex-local/run_T1281-M2478/blast_run_T1281-M2478/otu420068.txt
data/ilex-local/run_T1281-M2478/blast_run_T1281-M2478/otu420069.txt
data/ilex-local/run_T1281-M2478/blast_run_T1281-M2478/otu420070.txt
data/ilex-local/run_T1281-M2478/blast_run_T1281-M2478/otu420071.txt
data/ilex-local/run_T1281-M2478/blast_run_T1281-M2478/otu420072.txt
data/ilex-local/run_T1281-M2478/blast_run_T1281-M2478/otu420073.txt
data/ilex-local/run_T1281-M2478/blast_run_T1281-M2478/otu420074.txt
data/ilex-local/run_T1281-M2478/blast_run_T1281-M2478/otu420075.txt
data/ilex-local/run_T1281-M2478/blast_run_T1281-M2478/otu420076.txt
data/ilex-local/run_T1281-M2478/blast_run_T1281-M2478/otu420077.txt
data/ilex-local/run_T1281-M2478/blast_run_T1281-M2478/otu420078.txt
data/ilex-local/run_T1281-M2478/blast_run_T1281-M2478/otu420079.txt
data/ilex-local/run_T1281-M2478/blast_run_T1281-M2478/otu420080.txt
data/ilex-local/run_T1281-M2478/blast_run_T1281-M2478/otu420081.txt
data/ilex-local/run_T1281-M2478/blast_run_T1281-M2478/otu420082.txt
data/ilex-local/run_T1281-M2478/blast_run_T1281-M2478/otu420084.txt
data/ilex-local/run_T1281-M2478/blast_run_T1281-M2478/otu420085.txt
data/ilex-local/run_T1281-M2478/blast_run_T1281-M2478/otu420086.txt
data/ilex-local/run_T1281-M2478/blast_run_T1281-M2478/otu420087.txt
data/ilex-local/run_T1281-M2478/blast_run_T1281-M2478/otu420088.txt
data/ilex-local/run_T1281-M2478/blast_run_T1281-M2478/otu420089.txt
data/ilex-local/run_T1281-M2478/blast_run_T1281-M2478/otu420090.txt
data/ilex-local/run_T1281-M2478/blast_run_T1281-M2478/otu420091.txt
data/ilex-local/run_T1281-M2478/blast_run_T1281-M2478/otu420092.txt
data/ilex-local/run_T1281-M2478/blast_run_T1281-M2478/otu420093.txt
data/ilex-local/run_T1281-M2478/blast_run_T1281-M2478/otu420094.txt
data/ilex-local/run_T1281-M2478/blast_run_T1281-M2478/otu420095.txt
data/ilex-local/run_T1281-M2478/blast_run_T1281-M2478/otu420096.txt
data/ilex-local/run_T1281-M2478/blast_run_T1281-M2478/otu420097.txt
data/ilex-local/run_T1281-M2478/blast_run_T1281-M2478/otu420098.txt
data/ilex-local/run_T1281-M2478/blast_run_T1281-M2478/otu420100.txt
data/ilex-local/run_T1281-M2478/blast_run_T1281-M2478/otu420101.txt
data/ilex-local/run_T1281-M2478/blast_run_T1281-M2478/otu420102.txt
data/ilex-local/run_T1281-M2478/blast_run_T1281-M2478/otu420103.txt
data/ilex-local/run_T1281-M2478/blast_run_T1281-M2478/otu420104.txt
data/ilex-local/run_T1281-M2478/blast_run_T1281-M2478/otu420105.txt
data/ilex-local/run_T1281-M2478/blast_run_T1281-M2478/otu420106.txt
data/ilex-local/run_T1281-M2478/blast_run_T1281-M2478/otu420107.txt
data/ilex-local/run_T1281-M2478/blast_run_T1281-M2478/otu420108.txt
data/ilex-local/run_T1281-M2478/blast_run_T1281-M2478/otu420109.txt
data/ilex-local/run_T1281-M2478/blast_run_T1281-M2478/otu420110.txt
data/ilex-local/run_T1281-M2478/blast_run_T1281-M2478/otu420111.txt
data/ilex-local/run_T1281-M2478/blast_run_T1281-M2478/otu420112.txt
data/ilex-local/run_T1281-M2478/blast_run_T1281-M2478/otu420113.txt
data/ilex-local/run_T1281-M2478/blast_run_T1281-M2478/otu420114.txt
data/ilex-local/run_T1281-M2478/blast_run_T1281-M2478/tmp.fas
data/ilex-local/run_T1281-M2478/boot_summary.tre
data/ilex-local/run_T1281-M2478/logfile
data/ilex-local/run_T1281-M2478/muscle.log
data/ilex-local/run_T1281-M2478/new_seqs_UNaligned_2020-06-29_T1281-M2478.fas
data/ilex-local/run_T1281-M2478/new_seqs_aligned_2020-06-29_T1281-M2478.fas
data/ilex-local/run_T1281-M2478/original_T1281-M2478.fas
data/ilex-local/run_T1281-M2478/original_cleaned.fas
data/ilex-local/run_T1281-M2478/otu_info_T1281-M2478.json
data/ilex-local/run_T1281-M2478/physcraper_T1281-M2478.fas
data/ilex-local/run_T1281-M2478/physcraper_T1281-M2478.fas.reduced
data/ilex-local/run_T1281-M2478/random_resolve.tre
data/ilex-local/run_T1281-M2478/run.config
data/ilex-remote/inputs_T1281-M2478/mrca.txt
data/ilex-remote/inputs_T1281-M2478/otu_info_T1281-M2478.csv
data/ilex-remote/inputs_T1281-M2478/physcraper_T1281-M2478.fas
data/ilex-remote/inputs_T1281-M2478/physcraper_T1281-M2478.tre
data/ilex-remote/inputs_T1281-M2478/taxonname.fas
data/ilex-remote/inputs_T1281-M2478/taxonname.tre
data/ilex-remote/run_T1281-M2478/blast_run_T1281-M2478/otu420067.xml
data/ilex-remote/run_T1281-M2478/blast_run_T1281-M2478/otu420068.xml
data/ilex-remote/run_T1281-M2478/blast_run_T1281-M2478/otu420069.xml
data/ilex-remote/run_T1281-M2478/blast_run_T1281-M2478/otu420070.xml
data/ilex-remote/run_T1281-M2478/blast_run_T1281-M2478/otu420071.xml
data/ilex-remote/run_T1281-M2478/blast_run_T1281-M2478/otu420072.xml
data/ilex-remote/run_T1281-M2478/blast_run_T1281-M2478/otu420073.xml
data/ilex-remote/run_T1281-M2478/blast_run_T1281-M2478/otu420074.xml
data/ilex-remote/run_T1281-M2478/blast_run_T1281-M2478/otu420075.xml
data/ilex-remote/run_T1281-M2478/blast_run_T1281-M2478/otu420076.xml
data/ilex-remote/run_T1281-M2478/blast_run_T1281-M2478/otu420077.xml
data/ilex-remote/run_T1281-M2478/blast_run_T1281-M2478/otu420078.xml
data/ilex-remote/run_T1281-M2478/blast_run_T1281-M2478/otu420079.xml
data/ilex-remote/run_T1281-M2478/blast_run_T1281-M2478/otu420080.xml
data/ilex-remote/run_T1281-M2478/blast_run_T1281-M2478/otu420081.xml
data/ilex-remote/run_T1281-M2478/blast_run_T1281-M2478/otu420082.xml
data/ilex-remote/run_T1281-M2478/blast_run_T1281-M2478/otu420084.xml
data/ilex-remote/run_T1281-M2478/blast_run_T1281-M2478/otu420085.xml
data/ilex-remote/run_T1281-M2478/blast_run_T1281-M2478/otu420086.xml
data/ilex-remote/run_T1281-M2478/blast_run_T1281-M2478/otu420087.xml
data/ilex-remote/run_T1281-M2478/blast_run_T1281-M2478/otu420088.xml
data/ilex-remote/run_T1281-M2478/blast_run_T1281-M2478/otu420089.xml
data/ilex-remote/run_T1281-M2478/blast_run_T1281-M2478/otu420090.xml
data/ilex-remote/run_T1281-M2478/blast_run_T1281-M2478/otu420091.xml
data/ilex-remote/run_T1281-M2478/blast_run_T1281-M2478/otu420092.xml
data/ilex-remote/run_T1281-M2478/blast_run_T1281-M2478/otu420093.xml
data/ilex-remote/run_T1281-M2478/blast_run_T1281-M2478/otu420094.xml
data/ilex-remote/run_T1281-M2478/blast_run_T1281-M2478/otu420095.xml
data/ilex-remote/run_T1281-M2478/blast_run_T1281-M2478/otu420096.xml
data/ilex-remote/run_T1281-M2478/blast_run_T1281-M2478/otu420097.xml
data/ilex-remote/run_T1281-M2478/blast_run_T1281-M2478/otu420098.xml
data/ilex-remote/run_T1281-M2478/blast_run_T1281-M2478/otu420100.xml
data/ilex-remote/run_T1281-M2478/blast_run_T1281-M2478/otu420101.xml
data/ilex-remote/run_T1281-M2478/blast_run_T1281-M2478/otu420102.xml
data/ilex-remote/run_T1281-M2478/blast_run_T1281-M2478/otu420103.xml
data/ilex-remote/run_T1281-M2478/blast_run_T1281-M2478/otu420104.xml
data/ilex-remote/run_T1281-M2478/blast_run_T1281-M2478/otu420105.xml
data/ilex-remote/run_T1281-M2478/blast_run_T1281-M2478/otu420106.xml
data/ilex-remote/run_T1281-M2478/blast_run_T1281-M2478/otu420107.xml
data/ilex-remote/run_T1281-M2478/blast_run_T1281-M2478/otu420108.xml
data/ilex-remote/run_T1281-M2478/blast_run_T1281-M2478/otu420109.xml
data/ilex-remote/run_T1281-M2478/blast_run_T1281-M2478/otu420110.xml
data/ilex-remote/run_T1281-M2478/blast_run_T1281-M2478/otu420111.xml
data/ilex-remote/run_T1281-M2478/blast_run_T1281-M2478/otu420112.xml
data/ilex-remote/run_T1281-M2478/blast_run_T1281-M2478/otu420113.xml
data/ilex-remote/run_T1281-M2478/blast_run_T1281-M2478/otu420114.xml
data/ilex-remote/run_T1281-M2478/logfile
data/ilex-remote/run_T1281-M2478/otu_info_T1281-M2478.json
data/ilex-remote/run_T1281-M2478/run.config
data/ilex-test-local-1/blast_run_alignment_T1281_M2478_pruned/otu1.txt
data/ilex-test-local-1/blast_run_alignment_T1281_M2478_pruned/otu10.txt
data/ilex-test-local-1/blast_run_alignment_T1281_M2478_pruned/otu11.txt
data/ilex-test-local-1/blast_run_alignment_T1281_M2478_pruned/otu12.txt
data/ilex-test-local-1/blast_run_alignment_T1281_M2478_pruned/otu13.txt
data/ilex-test-local-1/blast_run_alignment_T1281_M2478_pruned/otu14.txt
data/ilex-test-local-1/blast_run_alignment_T1281_M2478_pruned/otu15.txt
data/ilex-test-local-1/blast_run_alignment_T1281_M2478_pruned/otu16.txt
data/ilex-test-local-1/blast_run_alignment_T1281_M2478_pruned/otu17.txt
data/ilex-test-local-1/blast_run_alignment_T1281_M2478_pruned/otu18.txt
data/ilex-test-local-1/blast_run_alignment_T1281_M2478_pruned/otu19.txt
data/ilex-test-local-1/blast_run_alignment_T1281_M2478_pruned/otu2.txt
data/ilex-test-local-1/blast_run_alignment_T1281_M2478_pruned/otu20.txt
data/ilex-test-local-1/blast_run_alignment_T1281_M2478_pruned/otu21.txt
data/ilex-test-local-1/blast_run_alignment_T1281_M2478_pruned/otu22.txt
data/ilex-test-local-1/blast_run_alignment_T1281_M2478_pruned/otu23.txt
data/ilex-test-local-1/blast_run_alignment_T1281_M2478_pruned/otu24.txt
data/ilex-test-local-1/blast_run_alignment_T1281_M2478_pruned/otu25.txt
data/ilex-test-local-1/blast_run_alignment_T1281_M2478_pruned/otu26.txt
data/ilex-test-local-1/blast_run_alignment_T1281_M2478_pruned/otu27.txt
data/ilex-test-local-1/blast_run_alignment_T1281_M2478_pruned/otu28.txt
data/ilex-test-local-1/blast_run_alignment_T1281_M2478_pruned/otu29.txt
data/ilex-test-local-1/blast_run_alignment_T1281_M2478_pruned/otu3.txt
data/ilex-test-local-1/blast_run_alignment_T1281_M2478_pruned/otu30.txt
data/ilex-test-local-1/blast_run_alignment_T1281_M2478_pruned/otu31.txt
data/ilex-test-local-1/blast_run_alignment_T1281_M2478_pruned/otu32.txt
data/ilex-test-local-1/blast_run_alignment_T1281_M2478_pruned/otu33.txt
data/ilex-test-local-1/blast_run_alignment_T1281_M2478_pruned/otu34.txt
data/ilex-test-local-1/blast_run_alignment_T1281_M2478_pruned/otu35.txt
data/ilex-test-local-1/blast_run_alignment_T1281_M2478_pruned/otu36.txt
data/ilex-test-local-1/blast_run_alignment_T1281_M2478_pruned/otu37.txt
data/ilex-test-local-1/blast_run_alignment_T1281_M2478_pruned/otu38.txt
data/ilex-test-local-1/blast_run_alignment_T1281_M2478_pruned/otu39.txt
data/ilex-test-local-1/blast_run_alignment_T1281_M2478_pruned/otu4.txt
data/ilex-test-local-1/blast_run_alignment_T1281_M2478_pruned/otu5.txt
data/ilex-test-local-1/blast_run_alignment_T1281_M2478_pruned/otu6.txt
data/ilex-test-local-1/blast_run_alignment_T1281_M2478_pruned/otu7.txt
data/ilex-test-local-1/blast_run_alignment_T1281_M2478_pruned/otu8.txt
data/ilex-test-local-1/blast_run_alignment_T1281_M2478_pruned/otu9.txt
data/ilex-test-local-1/blast_run_alignment_T1281_M2478_pruned/tmp.fas
data/ilex-test-local-1/inputs_alignment_T1281_M2478_pruned/mrca.txt
data/ilex-test-local-1/inputs_alignment_T1281_M2478_pruned/otu_info_alignment_T1281_M2478_pruned.csv
data/ilex-test-local-1/inputs_alignment_T1281_M2478_pruned/physcraper_alignment_T1281_M2478_pruned.fas
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data/schoch_ascomycota_1_2020.06.06/run_Tr5276-M3939-mod/blast_run_Tr5276-M3939-mod/otu63309.txt
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data/schoch_ascomycota_1_2020.06.06/run_Tr5276-M3939-mod/blast_run_Tr5276-M3939-mod/otu63320.txt
data/schoch_ascomycota_1_2020.06.06/run_Tr5276-M3939-mod/blast_run_Tr5276-M3939-mod/otu63321.txt
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data/schoch_ascomycota_2_2020.06.06/run_Tr5276-M3938-mod/blast_run_Tr5276-M3938-mod/otu63343.txt
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data/schoch_ascomycota_2_2020.06.06/run_Tr5276-M3938-mod/blast_run_Tr5276-M3938-mod/otu63345.txt
data/schoch_ascomycota_2_2020.06.06/run_Tr5276-M3938-mod/blast_run_Tr5276-M3938-mod/otu63346.txt
data/schoch_ascomycota_2_2020.06.06/run_Tr5276-M3938-mod/blast_run_Tr5276-M3938-mod/otu63347.txt
data/schoch_ascomycota_2_2020.06.06/run_Tr5276-M3938-mod/blast_run_Tr5276-M3938-mod/otu63350.txt
data/schoch_ascomycota_2_2020.06.06/run_Tr5276-M3938-mod/blast_run_Tr5276-M3938-mod/otu63352.txt
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data/schoch_ascomycota_2_2020.06.06/run_Tr5276-M3938-mod/blast_run_Tr5276-M3938-mod/otu63359.txt
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data/schoch_ascomycota_2_2020.06.06/run_Tr5276-M3938-mod/blast_run_Tr5276-M3938-mod/otu63433.txt
data/schoch_ascomycota_2_2020.06.06/run_Tr5276-M3938-mod/blast_run_Tr5276-M3938-mod/otu63434.txt
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data/schoch_ascomycota_2_2020.06.06/run_Tr5276-M3938-mod/blast_run_Tr5276-M3938-mod/otu63441.txt
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McTavishLab/physcraperex documentation built on April 10, 2021, 12:02 a.m.

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