PhyloCoco is an easy-to-use software designed for molecular phylogenetic estimation. It is a simple but efficient tool that can help researchers to determine the evolutionary relationships among various species by analyzing DNA and RNA sequences.
If you're looking for a free software tool for molecular phylogenetics, PhyloCoco may be a great choice. This minimalist tool is designed to rebuild phylogenies based on the likelihood criterion, making it a valuable resource for anyone studying evolutionary relationships among organisms.
One of the best things about PhyloCoco is that it automatically selects the best substitution model of DNA evolution for the dataset of sequences you want to analyze. Within a short period of time, you'll be able to see the best phylogeny that's been found.
In general, molecular phylogenetics is all about exploring hierarchical evolutionary relationships among organisms using molecular data. This information is typically represented using a weighted tree called a phylogeny. The leaves on the tree represent observed organisms, while the internal vertices represent intermediate ancestors. The edges represent the evolutionary relationships between pairs of organisms.
When you use PhyloCoco, you'll enjoy a number of key features. For example, the GTR model of DNA evolution is supported, and a gamma distribution is used to model among site rate heterogeneity. You'll have access to various optimization algorithms, including Random Directions, Brent's algorithm, and Random Search for unconstrained non-linear optimization of the likelihood parameters. Additionally, Very Large Scale Neighborhood (VLSN) search is used for the topology optimization, while Iterated Local Search (ILS) is used to explore the solution space. Finally, PhyloCoco uses PaloAlto to display the resulting phylogeny.
In terms of requirements, PhyloCoco runs best on a G4 or an intel core duo processor with Java 1.4 or higher. If you want to take advantage of all the recommended features, however, you might want to use an intel core 2 duo with Java 1.5 or higher.
Overall, PhyloCoco is a valuable software tool that can help you understand the evolutionary relationships between organisms. With its powerful optimization algorithms and automatic selection of substitution models, it's an efficient and effective way to explore molecular phylogenetics data.
One of the best things about PhyloCoco is that it automatically selects the best substitution model of DNA evolution for the dataset of sequences you want to analyze. Within a short period of time, you'll be able to see the best phylogeny that's been found.
In general, molecular phylogenetics is all about exploring hierarchical evolutionary relationships among organisms using molecular data. This information is typically represented using a weighted tree called a phylogeny. The leaves on the tree represent observed organisms, while the internal vertices represent intermediate ancestors. The edges represent the evolutionary relationships between pairs of organisms.
When you use PhyloCoco, you'll enjoy a number of key features. For example, the GTR model of DNA evolution is supported, and a gamma distribution is used to model among site rate heterogeneity. You'll have access to various optimization algorithms, including Random Directions, Brent's algorithm, and Random Search for unconstrained non-linear optimization of the likelihood parameters. Additionally, Very Large Scale Neighborhood (VLSN) search is used for the topology optimization, while Iterated Local Search (ILS) is used to explore the solution space. Finally, PhyloCoco uses PaloAlto to display the resulting phylogeny.
In terms of requirements, PhyloCoco runs best on a G4 or an intel core duo processor with Java 1.4 or higher. If you want to take advantage of all the recommended features, however, you might want to use an intel core 2 duo with Java 1.5 or higher.
Overall, PhyloCoco is a valuable software tool that can help you understand the evolutionary relationships between organisms. With its powerful optimization algorithms and automatic selection of substitution models, it's an efficient and effective way to explore molecular phylogenetics data.
What's New
Version 2.3: N/A