Quartet Sampling (w/ better RAxML-NG tempfile handling for runs with large --reps & --max-random-sample-proportion)
Quartet Sampling is a method to analyze molecular phylogenies by calculating branch support using repeated sampling of quartets. Quartet Sampling differs from other support methods by combining a set of of tests into a single, efficient framework to address phylogenetic discordance. QS is particularly useful for very large and data-sparse alignments or large phylogenomic datasets.
For runs with large --reps & --max-random-sample-proportion that select RAxML-NG as the engine, superfluous RAxML-NG job files are deleted as they're generated, c.f. the master branch where they accumulate until the end of the run. For my own dataset of ~500 loci (--reps > 3000, --max-random-sample-proportion > 0.5) this amounted to >1TB over the course of a run (which had to be provisioned for). The same dataset can be kept at ~12GB using the version in this fork; this is easier to fit/run in RAM.
Version 1.3.1 - Adds RESULTS.node.count.csv that provides counts and representative topologies for the three quartet arragements. This is useful when QD is low in determining the more common discordant option.
For complete details, see the manual for Quartet Sampling (https://github.com/FePhyFoFum/quartetsampling/blob/master/quartetsampling.pdf).
Shuiyin Liu has created a new R-script that can visualize QS results:
https://github.com/ShuiyinLIU/QS_visualization
Please reference his URL separately, if you use this visualization script.
James B Pease, Joseph W Brown, Joseph F Walker, Cody E Hinchliff, Stephen A Smith. 2018. Quartet Sampling distinguishes lack of support from conflicting support in the green plant tree of life. American Journal of Botany. 105(3): 385–403. doi:10.1002/ajb2.1016
Link to publication: http://dx.doi.org/10.1002/ajb2.1016
Please also include the URL (https://www.github.com/fephyfofum/quartetsampling).
Be sure also to cite RAxML-NG, RAxML, PAUP, or IQ-TREE (depending on which engine you use).
- James B. Pease - www.peaselab.org
- Stephen A. Smith blackrim.org
- Cody Hinchliff
- Joseph W. Brown
- Joseph F. Walker
This file is part of 'quartetsampling'
'quartetsampling' is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
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