In McTavishLab/physcraperex: Physcraper Workflow Examples

The Pxhyscraper tag

T1281-M2478

Input files

Physcraper rewrites input files for a couple reasons: reproducibility, taxon name matching, and taxon reconciliation. It also writes the config file down if none was provided.

Run files

Files in here are also automatically written down by Physcraper.

blast runs, alignments, raxml trees, bootstrap

The trees are reconstructed using RAxML, with tip labels corresponding to Physcraper taxon ids (e.g., otu42009, otuPS1) and not taxon names (e.g., Helwingia japonica), nor taxonomic ids (e.g., ott or ncbi). Branch lengths are proportional to relative substitution rates. The RAxML tree with taxon names as tip labels is saved on the outputs_tag folder.

par(mar=c(0.5,1,1,0.5), xpd=NA)

updated_tree_otus <- ape::read.tree(file = "../data/ilex-local/run_T1281-M2478/RAxML_bestTree.2020-06-29")
ape::plot.phylo(ape::ladderize(updated_tree_otus), type = "fan", cex = 0.25, label.offset = 0.01, edge.width = 0.5)
ape::add.scale.bar(cex = 0.3, font = 1, col = "black")
mtext("Updated tree - otu tags as labels", side = 3, line = 0)

Output files

A variety of files are automatically written down by Physcraper.

A nexson tree with all types of tip labels is saved in here. From this tree, a tree with any kind of label can be produced. By default, the updated tree with taxon names as tip labels is saved in the output_tag folder as updated_taxonname.tre.

Updated_sumtree and updated_tree_taxonname are the same tree: a consensus tree output of summtrees from DendroPy.

updated_sumtree <- ape::read.tree(file = "../data/pg_2827_tree6577/outputs_pg_2827tree6577/physcraper_pg_2827tree6577.tre")

updated_tree_taxonname <- ape::read.tree(
  file = "../data/pg_2827_tree6577/outputs_pg_2827tree6577/updated_taxonname.tre")
# ape::plot.phylo(ape::ladderize(updated_tree_taxonname), cex = 0.35)
# updated_tree_taxonname$tip.label %in% c("Helwingia_japonica_otu420083", "Helwingia_chinensis_otu420099")

# updated_raxml <- ape::read.tree(file = "../data/pg_2827_tree6577/run_pg_2827tree6577_run4/RAxML_bestTree.2020-07-31")
updated_sumtree_drop <- ape::drop.tip(updated_sumtree, c("otu420083", "otu420099"))

par(mar=c(0,1,2,0), xpd=NA)  # adjust margins for all plots after this?

ape::plot.phylo(ape::ladderize(updated_tree_taxonname), type = "fan", cex = 0.25, label.offset = 0.01, edge.width = 0.5)
ape::add.scale.bar(cex = 0.3, font = 1, col = "black")
mtext("Updated tree - Taxon names as labels  ", side = 3, line = 1)