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Full-Text Articles in Genetics and Genomics
Rasp 4: Ancestral State Reconstruction Tool For Multiple Genes And Characters, Yan Yu, Christopher Blair, Xingjin He
Rasp 4: Ancestral State Reconstruction Tool For Multiple Genes And Characters, Yan Yu, Christopher Blair, Xingjin He
Publications and Research
With the continual progress of sequencing techniques, genome-scale data are increasingly used in phylogenetic studies. With more data from throughout the genome, the relationship between genes and different kinds of characters is receiving more attention. Here, we present version 4 of RASP, a software to reconstruct ancestral states through phylogenetic trees. RASP can apply generalized statistical ancestral reconstruction methods to phylogenies, explore the phylogenetic signal of characters to particular trees, calculate distances between trees, and cluster trees into groups. RASP 4 has an improved graphic user interface and is freely available from http://mnh.scu.edu.cn/soft/blog/RASP (program) and https://github.com/sculab/RASP (source code).
Order, Please! Uncertainty In The Ordinal-Level Classification Of Chlorophyceae, Karolina Fucikova, Paul O. Lewis, Suman Neupane, Kenneth G. Karol, Louise A. Lewis
Order, Please! Uncertainty In The Ordinal-Level Classification Of Chlorophyceae, Karolina Fucikova, Paul O. Lewis, Suman Neupane, Kenneth G. Karol, Louise A. Lewis
Biological and Physical Sciences Department Faculty Works
Background. Chlorophyceae is one of three most species-rich green algal classes and also the only class in core Chlorophyta whose monophyly remains uncontested as gene and taxon sampling improves. However, some key relationships within Chlorophyceae are less clear-cut and warrant further investigation. The present study combined genome-scale chloroplast data and rich sampling in an attempt to resolve the ordinal classification in Chlorophyceae. The traditional division into Sphaeropleales and Volvocales (SV), and a clade containing Oedogoniales, Chaetopeltidales, and Chaetophorales (OCC) was of particular interest with the addition of deeply branching members of these groups, as well as the placement of several …