Long overdue scripts for analyzing morphological characters
Saturation: cite https://doi.org/10.1111/j.1469-185X.2012.00240.x Understanding phylogenetic incongruence: lessons from phyllostomid bats. Liliana M. Dávalos, Andrea L. Cirranello, Jonathan H. Geisler, Nancy B. Simmons Biological Reviews 87(4), 991-1041
Simulation, Gower distances, and statistical scaffold: cite https://doi.org/10.1093/sysbio/syu022 Integrating Incomplete Fossils by Isolating Conflicting Signal in Saturated and Non-Independent Morphological Characters Liliana M. Dávalos, Paúl M. Velazco, Omar M. Warsi, Peter D. Smits, Nancy B. Simmons Systematic Biology, Volume 63, Issue 4, July 2014, 582–600
Gower distances:
Running dissimilarity_morphology.R requires running simulation_morphology.R first.
Statistical scaffold:
Step 1: Running rax_scaffold.pl estimates backbone constrained morphological trees and requires a morphology character file, outgroup specification, and a file with Newick sample of molecular trees.
Step 2: Running rax_mulopt.pl estimates branch lengths from both morphological and molecular data on backbone constrained morphological trees (from step 1) and requires a combined morphology and molecular character file, outgroup specification, a partition file, and a file with Newick set of best trees obtained in the step 1.