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phylometh

Repo for code, problems, text, and other info for the PhyloMeth course in phylogenetic methods

phylometh_continuous

Continuous trait exercise for PhyloMeth

phylometh_correlated

For correlated traits

phylometh_discrete

Discrete trait exercise

phylometh_diversification

Diversification exercise

phylometh_genetreespeciestree

Exercises about gene tree species tree issues for PhyloMeth

phylometh_gettingtreesanddata

Exercise in getting trees and data for PhyloMeth course

phylometh_mixed

phylomethinfo

Website for PhyloMeth course

phylomethweek3

I did the homework, so stop complaining!

phylotar

An automated pipeline for retrieving orthologous DNA sequences from GenBank in R

phylotips

phyloview

Overview of the state of phylogenetic information for a group of organisms

phytools

piecewisesim

Simple R package for doing a piecewise tree simulation: simulate to a given time period, then simulate from each of the surviving taxa

popularitree

R package to subsample a tree to "popular" taxa by various metrics

prepotol

Prepare a tree for uploading to OpenTree

proteinevolver

Automatically exported from code.google.com/p/proteinevolver

purpleairpy

Python library to pull in information from Purpleair sensors

rateviz

A package for visualizing rate matrices. Original use case is visualizing matrices for diversitree and selac, but this is a more general solution.

reanalysis_zanne2014

this includes all scripts, analyses, and results of our re-analysis of Zanne et al. 2014 Nature 506: 89-92

recipes

Werner Family Recipes

replaceddig

Fostering independent graduate research

returnoftheminivan

Data for response to Donoghue and Edward's response to Beaulieu and O'Meara. We have more cupholders, and they come filled with data! [And cheerios]

rgithub

R bindings for the github API

rjs

R in JavaScript

rnsf

Unofficial package to interface with NSF API

rorcid

A programmatic interface the Orcid.org API

rotl

Interface to Open Tree of Life API

rredis

R client for Redis