# Emmanuel Paradis

#### 10 packages on CRAN

Functions for reading, writing, plotting, and manipulating phylogenetic trees, analyses of comparative data in a phylogenetic framework, ancestral character analyses, analyses of diversification and macroevolution, computing distances from DNA sequences, reading and writing nucleotide sequences as well as importing from BioConductor, and several tools such as Mantel's test, generalized skyline plots, graphical exploration of phylogenetic data (alex, trex, kronoviz), estimation of absolute evolutionary rates and clock-like trees using mean path lengths and penalized likelihood, dating trees with non-contemporaneous sequences, translating DNA into AA sequences, and assessing sequence alignments. Phylogeny estimation can be done with the NJ, BIONJ, ME, MVR, SDM, and triangle methods, and several methods handling incomplete distance matrices (NJ*, BIONJ*, MVR*, and the corresponding triangle method). Some functions call external applications (PhyML, Clustal, T-Coffee, Muscle) whose results are returned into R.

Flexible framework for coalescent analyses in R. It includes a main function running the MCMC algorithm, auxiliary functions for tree rearrangement, and some functions to compute population genetic parameters.

Functions for reading, writing, plotting, analysing, and manipulating allelic and haplotypic data, including from VCF files, and for the analysis of population nucleotide sequences and micro-satellites including coalescent analyses, linkage disequilibrium, population structure (Fst, Amova) and equilibrium (HWE), haplotype networks, minimum spanning tree and network, and median-joining networks.

Functions for fitting models of trait evolution on phylogenies for continuous traits. The majority of functions described in Thomas and Freckleton (2012) <doi:10.1111/j.2041-210X.2011.00132.x> and include functions that allow for tests of variation in the rates of trait evolution.

Functions for fitting models of trait evolution on phylogenies for continuous traits. The majority of functions described in Thomas and Freckleton (2011) <doi:10.1111/j.2041-210X.2011.00132.x> and include functions that allow for tests of variation in the rates of trait evolution.

Package contains methods for estimation of phylogenetic trees and networks using Maximum Likelihood, Maximum Parsimony, distance methods and Hadamard conjugation. Allows to compare trees, models selection and offers visualizations for trees and split networks.

Provides a base S4 class for comparative methods, incorporating one or more trees and trait data.

A collection of functions for data manipulation, plotting and statistical computing, to use separately or with the book "Visual Statistics. Use R!": Shipunov (2019) <http://ashipunov.info/shipunov/software/r/r-en.htm>. Most useful functions are probably Bclust(), Jclust() and BootA() which bootstrap hierarchical clustering; Recode...() which multiple recode in a fast, flexible and simple way; Misclass() which outputs confusion matrix even if classes are not concerted; Overlap() which calculates overlaps of convex hulls from any projection; and Pleiad() which is fast and flexible correlogram. In fact, there are much more useful functions, please see documentation.

Searches for phylogenetic trees that are optimal using a user-defined criterion. Implements Profile Parsimony (Faith and Trueman, 2001) <doi:10.1080/10635150118627>, and Successive Approximations (Farris, 1969) <doi:10.2307/2412182>. Handles inapplicable data using the algorithm of Brazeau, Guillerme and Smith (2019) <doi:10.1093/sysbio/syy083>.

Efficient implementations of functions for the creation, modification and analysis of phylogenetic trees. Applications include: generation of trees with specified shapes; rooting of trees and extraction of subtrees; calculation and depiction of node support; calculation of ancestor-descendant relationships; import and export of trees from Newick, Nexus (Maddison et al. 1997) <doi:10.1093/sysbio/46.4.590>, and TNT <http://www.lillo.org.ar/phylogeny/tnt/> formats; and analysis of partitions and partition information.