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Biopython: freely available Python tools for computational molecular biology and bioinformatics
- P. Cock, T. Antão, +8 authors Michiel J. L. de Hoon
- Computer Science, Medicine
- 20 March 2009
Biopython includes modules for reading and writing different sequence file formats and multiple sequence alignments, dealing with 3D macro molecular structures, interacting with common tools such as BLAST, ClustalW and EMBOSS, accessing key online databases, as well as providing numerical methods for statistical learning. Expand
Reconstructing the early evolution of Fungi using a six-gene phylogeny
It is indicated that there may have been at least four independent losses of the flagellum in the kingdom Fungi, and the enigmatic microsporidia seem to be derived from an endoparasitic chytrid ancestor similar to Rozella allomycis, on the earliest diverging branch of the fungal phylogenetic tree. Expand
Phylogeny of the Gyalectales and Ostropales (Ascomycota, Fungi): among and within order relationships based on nuclear ribosomal RNA small and large subunits.
Bayesian inference of phylogeny recovered the same topology as a conventional heuristic search using Maximum Likelihood as the optimization criterion and seems superior to bootstrapping in estimating support for short internal branches. Expand
A phylogenetic estimation of trophic transition networks for ascomycetous fungi: are lichens cradles of symbiotrophic fungal diversification?
Use of phylogenetic analyses that incorporate these newly recovered fungi and ancestral state reconstructions that take into account phylogenetic uncertainty provide the basis for estimating trophic transition networks in the Ascomycota and provide a first set of hypotheses regarding the evolution of symbiotrophy and saprotrophy in the most species-rich fungal phylum. Expand
Assembling the fungal tree of life: progress, classification, and evolution of subcellular traits.
- F. Lutzoni, F. Kauff, +41 authors R. Vilgalys
- Biology, Medicine
- American journal of botany
- 1 October 2004
This study provides a phylogenetic synthesis for the Fungi and a framework for future phylogenetic studies on fungi and the impact of this newly discovered phylogenetic structure on supraordinal classifications is discussed. Expand
The Ascomycota tree of life: a phylum-wide phylogeny clarifies the origin and evolution of fundamental reproductive and ecological traits.
A 6-gene, 420-species maximum-likelihood phylogeny of Ascomycota, the largest phylum of Fungi, and a phylogenetic informativeness analysis of all 6 genes and a series of ancestral character state reconstructions support a terrestrial, saprobic ecology as ancestral are presented. Expand
A multigene phylogenetic synthesis for the class Lecanoromycetes (Ascomycota): 1307 fungi representing 1139 infrageneric taxa, 317 genera and 66 families.
- J. Miadlikowska, F. Kauff, +29 authors S. Stenroos
- Biology, Medicine
- Molecular phylogenetics and evolution
- 1 October 2014
A multigene phylogenetic synthesis of the Lecanoromycetes based on 642 newly generated and 3329 publicly available sequences revealing relatively stable relationships for many families and orders is provided. Expand
Systematic analysis of the twin cx(9)c protein family.
- Sebastian Longen, Melanie Bien, +6 authors J. Riemer
- Biology, Medicine
- Journal of molecular biology
- 23 October 2009
The data suggest that already early during the evolution of eukaryotic cells, a multitude of twin Cx(9)C proteins developed, which exhibit largely nonredundant roles critical for the biogenesis of enzymes of the respiratory chain in mitochondria. Expand
New insights into classification and evolution of the Lecanoromycetes (Pezizomycotina, Ascomycota) from phylogenetic analyses of three ribosomal RNA- and two protein-coding genes.
The phylogenies confirm that ascus morphology cannot be applied consistently to shape the classification of lichen-forming fungi and conclude that a phylogenetic synthesis for a chosen taxonomic group should include a comprehensive assessment of phylogenetic confidence based on multiple estimates using different methods and on a progressive taxon sampling with an increasing number of taxa, even if it involves an increasing amount of missing data. Expand
Phylogenetic affiliations of members of the heterogeneous lichen-forming fungi of the genus Lecidea sensu Zahlbruckner (Lecanoromycetes, Ascomycota)
The phylogenetic placement of members of this heterogeneous group of lichen-forming fungi is elucidated to improve the classification and phylogeny of Lecanoromycetes and the new combination Frutidella pullata is proposed here. Expand