Skip to content

Tutorials

Jump to bottom
Daniel Portik edited this page Mar 25, 2020 · 2 revisions

SuperCRUNCH Tutorials

There are currently nine tutorials, which cover the full range of analyses run in the SuperCRUNCH publication. These tutorials can be found on the OSF SuperCRUNCH project page. Each tutorial includes all data and instructions necessary to replicate the analysis. These tutorials are named to match the names of the analyses described in the Supplemental Materials of Portik & Wiens (2020).

The tutorials include:

  • Iguania-Fast: Construct a very large species-level supermatrix for Iguania using "fast" settings.

    • Produces supermatrix with 60 loci, 1,399 species, 12,978 sequences.
    • Takes ~1.5 hours to run and requires 15GB of space.
    • Difficulty: Medium.
    • Link: https://osf.io/x5hrm/

  • Iguania-Thorough: Construct a very large species-level supermatrix for Iguania using "thorough" settings.

    • Produces supermatrix with 61 loci, 1,426 species, 13,307 sequences.
    • Takes ~13 hours to run and requires 30GB of space.
    • Difficulty: Hard.
    • Link: https://osf.io/9gs32/

  • Kaloula-Vouchered: Construct a vouchered population-level UCE phylogenomic supermatrix.

    • Produces supermatrix with 1,784 loci, 18 vouchered samples, 28,790 sequences.
    • Takes ~20 minutes to run and requires 350MB of space.
    • Difficulty: Easy.
    • Link: https://osf.io/zxnq8/

  • Kaloula-Species: Construct a species-level UCE phylogenomic supermatrix, which is a variation of the above tutorial.

    • Produces supermatrix with 1,784 loci, 14 species, 22,717 sequences.
    • Takes ~20 minutes to run and requires 350MB of space.
    • Difficulty: Easy.
    • Link: https://osf.io/crzp5/

  • Trachylepis-Vouchered: Reconstruct a vouchered multi-locus phylogeography dataset from a published study.

    • Produces dataset with 4 loci, 108 vouchered samples, 400 sequences.
    • Takes ~1 minute to run and requires 10MB of space.
    • Difficulty: Easy.
    • Link: https://osf.io/bgc5z/

  • Trachylepis-Species: Construct a species-level supermatrix from a published phylogeography dataset.

    • Produces supermatrix with 4 loci, 7 species, 26 sequences.
    • Takes ~1 minute to run and requires 10MB of space.
    • Difficulty: Easy.
    • Link: https://osf.io/umswn/

  • Callisaurus-Population: Construct a de novo multi-locus population-level dataset from multiple published sources.

    • Produces dataset with 7 loci and 265 sequences. Samples are NOT linked by voucher codes.
    • Takes ~1 minute to run and requires 150MB of space.
    • Difficulty: Easy.
    • Link: https://osf.io/7gujb/

  • Uma-Population: Construct a de novo multi-locus population-level dataset from multiple published sources.

    • Produces dataset with 5 loci and 234 sequences. Samples are NOT linked by voucher codes.
    • Takes ~1 minute to run and requires 75MB of space.
    • Difficulty: Easy.
    • Link: https://osf.io/e28tu/

  • Hyperoliid-Outgroup: Incorporate published outgroup sequences from GenBank with unpublished ingroup sequences to create a custom supermatrix.

    • Produces supermatrix with 6 loci, 365 samples, 1,724 sequences.
    • Takes ~5 minutes to run and requires 100MB of space.
    • Difficulty: Medium.
    • Link: https://osf.io/q9nyx/
Clone this wiki locally