ProSeq

ProSeq prepares and analyzes large-scale DNA polymorphism datasets for evolutionary genetic and molecular ecology studies.

Key Features:

• File Format Support: The program supports over two dozen file formats for sequence polymorphism data.
• Sequence Editor: A flexible sequence editor is included for dataset preparation and manipulation.
• Data Visualization: Various tools for data visualization are included, such as visual illustration of phylogeny shapes generated with coalescent simulations.
• Quality Control: Tools for quality control of sequence polymorphism datasets are included.
• NJ-Phylogeny Reconstruction: Neighbor-joining phylogeny reconstruction is supported for evolutionary analysis.
• DNA Polymorphism Analyses: Most commonly used DNA polymorphism analyses are included.
• Coalescent Simulations: Coalescent simulations are supported for generating phylogenies under different scenarios.
• Command Line Tools: Command line tools such as vcf2fasta are provided for integration into bioinformatic pipelines.

Scientific Applications:

• Evolutionary Genetics: Preparation and evolutionary genetic analyses of genome- or transcriptome-scale sequence polymorphism datasets.
• Molecular Ecology: Processing and analysis of large-scale DNA polymorphism datasets for molecular ecology research.
• Teaching: Visual illustration of different shapes of phylogenies generated with coalescent simulations in different scenarios.

Methodology:

Sequence alignment, NJ-phylogeny reconstruction, DNA polymorphism analyses, and coalescent simulations.