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Demonstrating the phylotaR pipeline

A series of scripts for demonstrating the phylotaR pipeline for primates and palms. The scripts will first run the phylotaR pipeline and then generate alignments and trees.

Requirements

  • R (version 3+)
  • R packages: phylotaR, ape and treeman
  • BLAST+
  • RAxML
  • MAFFT

Install specific phylotaR release

# this will install the exact development version used to generate results
devtools::install_github(repo='AntonelliLab/phylotaR', ref='5677e1560f7b0f8f60e5109072d5af0326338d69')
# the code is not guarranteed to work with any other version

Folder set-up

- palms
- - [contains all palms phylotaR output]
- primates
- - [contains all primates phylotaR output]
- expected
- - [expected trees of palms and primates]
- figures
- - [tree viz output]
- taxdump.tar.gz
- ncbi-blast-2.7.1+
- - bin
- - - [contains BLAST+ executables]

taxdump.tar.gz can be downloaded from ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/ ncbi-blast-2.7.1+ can be downloaded from ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/. Download *-src.tar.gz, and extract. Note, the version number may be different for you and will need changed in the R scripts. Alternatively these arguments can be left blank in the run_*.R scripts and BLAST tools from the system path will be used and phylotaR will download the taxonomy itself.

Scripts

  • 0_run_*.R: Intiate the phylotaR pipeline.
  • 1_cluster_selection_*.R: Select clusters for alignments and run alignments with MAFFT
  • 2_supermatrix_*.R: Generate supermatrices from alignments and run RAxML
  • 3_visualise_*.R: Visualise the best RAxML tree and compare to expected trees

Each R script must be run manually.

Figures

Genus-level trees generated from the two 'best' phylotaR clusters for palms and primates.

Palms

Palms

Family-level comparison

Expected tree from Baker et al. (2009) Complete Generic-Level Phylogenetic Analyses of Palms (Arecaceae) with Comparisons of Supertree and Supermatrix Approaches. Systematic Biology, 58(2):240–256 DOI

Palms

Primates

Primates

Comparison

Expected tree from Perelman et al. (2011) A Molecular Phylogeny of Living Primates. PLOS Genetics DOI

Primates