Botany & Plant Sciences

This guide contains research resources for the study of botany and plant systematics.

Systematics Software

Delta
The DELTA format (DEscription Language for TAxonomy) is a flexible method for encoding taxonomic descriptions for computer processing. DELTA-format data can be used to produce natural-language descriptions, conventional or interactive keys, cladistic or phenetic classifications, and information-retrieval systems.
MacClade (Maddison & Maddison)
MacClade is a computer program for phylogenetic analysis written by David Maddison and Wayne Maddison. Its analytical strength is in studies of character evolution. It also provides many tools for entering and editing data and phylogenies, and for producing tree diagrams and charts.
PHYLIP (J. Felsenstein)
PHYLIP is a free package of programs for inferring phylogenies. It is distributed as source code, documentation files, and a number of different types of executables.
Sequin (NCBI)
Sequin is a stand-alone software tool developed by the NCBI for submitting and updating entries to the GenBank sequence database.
MAFFT (Multiple Alignment using Fast Fourier Transform)
MAFFT (Multiple Alignment using Fast Fourier Transform) is a high speed multiple sequence alignment program. Provided by the European Bioinformatics Institute (EMBL-EBI).
MUSCLE (MUltiple Sequence Comparison by Log- Expectation)
MUSCLE stands for MUltiple Sequence Comparison by Log- Expectation. MUSCLE is claimed to achieve both better average accuracy and better speed than ClustalW2 or T-Coffee, depending on the chosen options. Provided by the European Bioinformatics Institute (EMBL-EBI).
Mesquite
Mesquite is modular, extendible software for evolutionary biology, designed to help biologists organize and analyze comparative data about organisms. Its emphasis is on phylogenetic analysis, but some of its modules concern population genetics, while others do non-phylogenetic multivariate analysis. Because it is modular, the analyses available depend on the modules installed.
RAxML (Randomized Axelerated Maximum Likelihood)
RAxML-VI-HPC (randomized axelerated maximum likelihood for high performance computing) is a sequential and parallel program for inference of large phylogenies with maximum likelihood (ML).
CyVerse (formerly iPlant)
Our mission is to design, deploy, and expand a national cyberinfrastructure for life sciences research, and to train scientists in its use.
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CyVerse is funded by the National Science Foundation’s Directorate for Biological Sciences. We are a dynamic virtual organization led by the University of Arizona to fulfill a broad mission that spans our partner institutions: Texas Advanced Computing Center, Cold Spring Harbor Laboratory, and the University of North Carolina at Wilmington.