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Biopython: freely available Python tools for computational molecular biology and bioinformatics
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.
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.
Assembling the fungal tree of life: progress, classification, and evolution of subcellular traits.
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.
The archaebacterial origin of eukaryotes
- C. Cox, P. Foster, R. Hirt, S. Harris, T. Embley
- BiologyProceedings of the National Academy of Sciences
- 23 December 2008
The analyses favor a topology that supports the eocyte hypothesis rather than archaebacterial monophyly and the 3-domains tree of life, which is thought to be central to understanding the evolution of the eukaryotic cell.
An archaeal origin of eukaryotes supports only two primary domains of life
These results provide support for only two primary domains of life—Archaea and Bacteria—because eukaryotes arose through partnership between them.
Moss diversity: A molecular phylogenetic analysis of genera
This study presents phylogenetic and molecular phylogenetic diversity analyses of moss taxa from a total of 655 genera of mosses, and highlights the possible non-monophyly of many taxonomic families, particularly in the haplolepideous and pleurocarpous mosses.
A congruent phylogenomic signal places eukaryotes within the Archaea
- T. Williams, P. Foster, T. Nye, C. Cox, T. Embley
- BiologyProceedings of the Royal Society B: Biological…
- 24 October 2012
The results provide no support for the iconic three-domain tree of life, but are consistent with an extended eocyte hypothesis whereby vital components of the eukaryotic nuclear lineage originated from within the archaeal radiation.
Chloroplast Phylogeny of Asplenioid Ferns based on rbcL and trnL-F Spacer Sequences (Polypodiidae, Aspleniaceae) and its Implications for Biogeography
A phylogenetic framework from which the historical biogeography of asplenioid ferns can be inferred for Europe and North America is presented, showing a separation of the deeper branches into tropical and temperate clades.
Phylogenetic Relationships among the Mosses Based on Heterogeneous Bayesian Analysis of Multiple Genes from Multiple Genomic Compartments
The phylogenetic hypothesis for morphological evolution in mosses include a pseudopodium has arisen independently in Sphagnum and Andreaea, and the mucilage hairs of Andreaeobryum and Takakia are non-homologous, and that stomata were absent in the ancestor of all mosses.
Three geographically separate domestications of Asian rice.
By examining the footprints of selection in the genomes of different cultivated rice types, it is shown that there were three independent domestications in different parts of Asia, and it is concluded that aromatic rice is a result of a hybridization between japonica and aus, and that the tropical and temperate versions ofJaponica are later adaptations of one crop.