ape - Analyses of Phylogenetics and Evolution

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.

Last updated 1 months ago

openblascpp

17.11 score 57 stars 574 dependents 13k scripts 102k downloads

pegas - Population and Evolutionary Genetics Analysis System

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.

Last updated 1 years ago

7.53 score 18 dependents 564 scripts 5.6k downloads

tigers - Integration of Geography, Environment, and Remote Sensing

Handling and manipulation polygons, coordinates, and other geographical objects. The tools include: polygon areas, barycentric and trilinear coordinates (Hormann and Floater, 2006, <doi:10.1145/1183287.1183295>), convex hull for polygons (Graham and Yao, 1983, <doi:10.1016/0196-6774(83)90013-5>), polygon triangulation (Toussaint, 1991, <doi:10.1007/BF01905693>), great circle and geodesic distances, Hausdorff distance, and reduced major axis.

Last updated 4 months ago

fortran

3.40 score 1 scripts 227 downloads

voronoifortune - Voronoi Tessellation by Fortune Algorithm

Fortune's (1987, <doi:10.1007/BF01840357>) algorithm is a very efficient method to perform Voronoi tessellation and Delaunay triangulation. This package is a port of the original code published in the early 1990's by Steven Fortune.

Last updated 9 days ago

3.18 score

coalescentMCMC - MCMC Algorithms for the Coalescent

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. Extended description can be found in Paradis (2020) <doi:10.1201/9780429466700>. For details on the MCMC algorithm, see Kuhner et al. (1995) <doi:10.1093/genetics/140.4.1421> and Drummond et al. (2002) <doi:10.1093/genetics/161.3.1307>.

Last updated 3 years ago

2.56 score 18 scripts 250 downloads

distory - Distance Between Phylogenetic Histories

Geodesic distance between phylogenetic trees and associated functions. The theoretical background of 'distory' is published in Billera et al. (2001) "Geometry of the space of phylogenetic trees." <doi:10.1006/aama.2001.0759>.

Last updated 3 months ago

cpp

2.49 score 1 stars 3 dependents 34 scripts 355 downloads