Sakpuntoon, Varunya Srathongporn, Nathida Pontes, Ana Khunnamwong, Pannida Aires, Andreia Limtong, Savitree Gonçalves, Carla Gonçalves, Paula Sampaio, José Paulo Srisuk, Nantana
...
Published in
International journal of systematic and evolutionary microbiology
Two novel ascomycetous yeast species of the genus Wickerhamiella are proposed based on isolates obtained in Thailand from food waste and the fruiting body of a polypore fungus, and on a combination of conventional DNA-barcode sequence analyses and whole-genome phylogenies. We focus on a particular subclade of the genus Wickerhamiella that contains ...
Liang, KYH Orata, FD Boucher, YF Case, RJ
10.3389/fmicb.2021.683109 / Frontiers in Microbiology / 12 / 683109- / Switzerland
Liang, Kevin Y. H. Orata, Fabini D. Boucher, Yann F. Case, Rebecca J.
Published in
Frontiers in Microbiology
The family Rhodobacteraceae consists of alphaproteobacteria that are metabolically, phenotypically, and ecologically diverse. It includes the roseobacter clade, an informal designation, representing one of the most abundant groups of marine bacteria. The rapid pace of discovery of novel roseobacters in the last three decades meant that the best pra...
Meinel, Thomas Krause, Antje
Published in
Evolutionary bioinformatics online
In the last two decades, a large number of whole-genome phylogenies have been inferred to reconstruct the Tree of Life (ToL). Underlying data models range from gene or functionality content in species to phylogenetic gene family trees and multiple sequence alignments of concatenated protein sequences. Diversity in data models together with the use ...
Jun, Se-Ran Sims, Gregory E Wu, Guohong A Kim, Sung-Hou
Published in
Proceedings of the National Academy of Sciences of the United States of America
We present a whole-proteome phylogeny of prokaryotes constructed by comparing feature frequency profiles (FFPs) of whole proteomes. Features are l-mers of amino acids, and each organism is represented by a profile of frequencies of all features. The selection of feature length is critical in the FFP method, and we have developed a procedure for ide...
Wu, Guohong Albert Jun, Se-Ran Sims, Gregory E Kim, Sung-Hou
Published in
Proceedings of the National Academy of Sciences of the United States of America
The vast sequence divergence among different virus groups has presented a great challenge to alignment-based sequence comparison among different virus families. Using an alignment-free comparison method, we construct the whole-proteome phylogeny for a population of viruses from 11 viral families comprising 142 large dsDNA eukaryote viruses. The met...
Sims, Gregory E Jun, Se-Ran Wu, Guohong A Kim, Sung-Hou
Published in
Proceedings of the National Academy of Sciences of the United States of America
For comparison of whole-genome (genic + nongenic) sequences, multiple sequence alignment of a few selected genes is not appropriate. One approach is to use an alignment-free method in which feature (or l-mer) frequency profiles (FFP) of whole genomes are used for comparison-a variation of a text or book comparison method, using word frequency profi...
