rstats

Gaius

Divide and conquer phylogenetic supermatrices and supertrees in R.

outsider: Install and Run Programs, Outside of R, Inside of R

Outsider

Install and Run Programs, Outside of R, Inside of R.

restez

Create and Query a Local Copy of GenBank in R.

phylotaR

Automated Retrieval of Orthologous DNA Sequences from GenBank.

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

Access content Open-access! Abstract: The exceptional increase in molecular DNA sequence data in open repositories is mirrored by an ever-growing interest among evolutionary biologists to harvest and use those data for phylogenetic inference. Many quality issues, however, are known and the sheer amount and complexity of data available can pose considerable barriers to their usefulness. A key issue in this domain is the high frequency of sequence mislabeling encountered when searching for suitable sequences for phylogenetic analysis.

restez: Create and Query a Local Copy of GenBank in R

treeman

An R package for manipulating phylogentic trees.

Phylogenetic factorization of compositional data yields lineage-level associations in microbiome datasets

treeman: an R package for efficient and intuitive manipulation of phylogenetic trees

Access content Open-access! Abstract: BACKGROUND: Phylogenetic trees are hierarchical structures used for representing the inter-relationships between biological entities. They are the most common tool for representing evolution and are essential to a range of fields across the life sciences. The manipulation of phylogenetic trees-in terms of adding or removing tips-is often performed by researchers not just for reasons of management but also for performing simulations in order to understand the processes of evolution.