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Code base for Mammalia backbone-and-patch supermatrix project
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Fig1_circlePlottedTree
Fig2_treeOverview update to Figs Dec 2, 2019
Fig3_compare_NDexp-FBD update to Figs Dec 2, 2019
Fig4_compare_divTimes updates to Fig1-6 margins Oct 4, 2019
Fig5_compare_LTTs update to Figs Dec 2, 2019
Fig6_compare_tipDRs update to Figs Dec 2, 2019
FigS1-S10 update to Figs Dec 2, 2019
MoviesS1-S4 full updated MamPhy_v1 codebase Oct 2, 2019
_DATA updates to Fig1-6 margins Oct 4, 2019
_Fig1-6_toUpload update to Figs Dec 2, 2019
source_functions full updated MamPhy_v1 codebase Oct 2, 2019
zBLAST-to-MamPhy update to Figs Dec 2, 2019
.DS_Store update to Figs Dec 2, 2019
.gitattributes updates to Fig1-6 margins Oct 4, 2019
MS1_Fig1_circleTreePlotting.R full updated MamPhy_v1 codebase Oct 2, 2019
MS1_Fig2_treeOverview.R full updated MamPhy_v1 codebase Oct 2, 2019
MS1_Fig3_compare_NDexp-FBD.R full updated MamPhy_v1 codebase Oct 2, 2019
MS1_Fig4_compare_divTimes.R full updated MamPhy_v1 codebase Oct 2, 2019
MS1_Fig5_compare_LTTs.R full updated MamPhy_v1 codebase Oct 2, 2019
MS1_Fig6_compare_tipDRs.R full updated MamPhy_v1 codebase Oct 2, 2019
MS1_FigS1-S10_plotting.R full updated MamPhy_v1 codebase Oct 2, 2019
MS1_MoviesS1-S4_treeUncertainty.R full updated MamPhy_v1 codebase Oct 2, 2019
MS1_analyses_tipDR-calculations.R test Oct 2, 2019
MS1_analyses_treeAssembly.R full updated MamPhy_v1 codebase Oct 2, 2019
README.md update to Readme Dec 2, 2019

README.md

MamPhy_v1

Code base for Mammalia backbone-and-patch supermatrix project

Explore the mammal trees here.

References:

Upham NS, Esselstyn JA, Jetz W. 2019. Inferring the mammal tree: species-level sets of phylogenies for questions in ecology, evolution, and conservation. PLOS Biology https://doi.org/10.1371/journal.pbio.3000494

Data Dryad: https://doi.org/10.5061/dryad.tb03d03

Phylosubsetting tool: http://vertlife.org/phylosubsets (prune to taxa and download trees)

The enclosed code should enable all the analyses and figures in our PLOS Biology paper to be directly reproduced.

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