ptitle

veryfasttree

Efficient phylogenetic tree inference for massive taxonomic datasets

PhyInformR

PhyInformR package

TAPER

Two-dimensional outlier detection algorithm for pinpointing errors in small species-specific stretches of the multiple sequence alignments

USE

A R package to perform uniform sampling in the environmental space

SEM_SDMs

Reproducible framework to apply SEM to SDM exercise

AleRax

Gene tree - species tree reconciliation from gene tree distributions

PCAtest

R package PCAtest for evaluating the statistical significance of PCA analysis, selecting number of significant PC axes, and testing the contributions of the variables to those PCs.

lab-website-template

An easy-to-use, flexible website template for labs.

cauphy

cauphy R package

TaxonomyAlign

Taxonomy-guided multiple sequence alignment for difficult genes, including 12S and 16S mitochondrial rRNA.

SuperCRUNCH

A bioinformatics package for creating, filtering, and manipulating supermatrices and phylogenetic datasets using GenBank and/or local sequence data.

spfilteR

Semiparametric Spatial Filtering with Eigenvectors in (Generalized) Linear Models

mcl

MCL, the Markov Cluster algorithm, also known as Markov Clustering, is a method and program for clustering weighted or simple networks, a.k.a. graphs.

Asteroid

mop

GradME

Leaping through tree space: continuous phylogenetic inference for rooted and unrooted trees

MD-Cat

MD-Cat: Molecular Dating using Categorical model

lsd2

A phylogeny dating method using least-squares algorithms and criteria

Rlsd2

An R-wrapper for lsd2

shiftPlot

evorates

R package implementing methods for fitting "relaxed" models of continuous trait evolution to comparative data (i.e., a phylogeny and associated trait data), whereby the rate of trait evolution itself gradually changes over time and across lineages. Provides additional tools for simulating data, as well as manipulating, analyzing, and visualizing estimated model parameters.

seastaR

Source code for the R package seastaR, written by Lara Breithaupt and Mark Hibbins (see Hibbins et al. 2023). This package builds a gene tree variance-covariance matrix that can be used for downstream phylogenetic comparative analyses. Also included is a trait simulator and a function for maximum-likelihood estimation of the evolutionary rate.

speciesgeocodeR

Preparation of species occurrences and distribution data for the use in phylogenetic analyses. SpeciesgeocodeR is built for data exploration and data analysis and especially suited for biogeographical and ecological questions on large datasets. The package includes the easy creation of summary-tables and -graphs and geographical maps, the calculating of coexistence matrices and species ranges (EOO) as well as mapping diversity in geographic areas.

colourvalues

R library for assigning colours to values

covsel

Embedded covariate selection procedure for species distribution modelling

HMMerge

anglr

Mesh creation and topology for spatial data (and not just geographic)

sfdct

Decompose sf polygons into teeny triangles with four corners

PointedSDMs

Wrapper function for 'inlabru' for modeling species distribution models from disparate datasets.

posterior_polygons

Constructs polygons for point sets generated by posterior sampling