TREE-PUZZLE: maximum likelihood phylogenetic analysis using
  quartets and parallel computing

Schmidt, Heiko A.; Strimmer, Korbinian; Vingron, Martin; Haeseler, Arndt von

doi:10.1093/bioinformatics/18.3.502

Cited by 2,362 publications

(1,779 citation statements)

References 20 publications

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“…A multiple sequence alignment was constructed using the MUSCLE program and gap removal by in-house script based on the BLOSUM62 scoring matrix. The maximum likelihood tree reconstruction program TREE-PUZ-ZLE 49 (quartet puzzling, WAG model, estimated gama distribution rate with 1000 puzzling step) was used for phylogenetic tree reconstruction. The tree was well supported by 1,000 bootstraps in each node.…”

Section: Methodsmentioning

confidence: 99%

Genome sequence of the recombinant protein production host Pichia pastoris

et al. 2009

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The methylotrophic yeast Pichia pastoris is widely used for the production of proteins and as a model organism for studying peroxisomal biogenesis and methanol assimilation. P. pastoris strains capable of human-type N-glycosylation are now available, which increases the utility of this organism for biopharmaceutical production. Despite its biotechnological importance, relatively few genetic tools or engineered strains have been generated for P. pastoris. To facilitate progress in these areas, we present the 9.43 Mbp genomic sequence of the GS115 strain of P. pastoris. We also provide manually curated annotation for its 5,313 protein-coding genes.The methylotrophic yeast Pichia pastoris is by far the most commonly used yeast species in the production of recombinant proteins 1 and is employed in laboratories around the world to produce proteins for basic research and medical applications. It is also an important model organism for the investigation of peroxisomal proliferation and methanol assimilation. The P. pastoris expression technology has been commercially available for many years. P. pastoris grows to high cell density, provides tightly controlled methanol-inducible transgene expression and efficiently secretes heterologous proteins in defined media. Several P. pastoris-produced biopharmaceuticals that are either not glycosylated (such as human serum albumin 2 ) or for which glycosylation is needed only for proper folding (such as several vaccines 3 ) are already on the market. An important recent breakthrough has been the development of P. pastoris strains with humantype N-glycosylation [4][5][6] . Humanized glycosylation will further increase the importance of P. pastoris for biopharmaceutical production; indeed, proteins produced with this system are moving into clinical development 7 . Moreover, monoclonal antibodies can be made at gramper-liter scale in the humanized glycosylation-homogenous strains 8 .For further strain engineering, a better understanding of all aspects of the yeast's protein production machinery is needed, and a number of studies relating to P. pastoris's secretory system and engineered promoters have been forthcoming 9,10 . To facilitate the investigation of P. pastoris and other methylotrophic yeasts, we present the 9.43 Mbp genomic sequence of the GS115 strain of P. pastoris.

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Section: Methodsmentioning

confidence: 99%

Genome sequence of the recombinant protein production host Pichia pastoris

et al. 2009

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“…Bootstrap support values were estimated using 100 pseudo-replicates. For distance analyses, maximum likelihood distances were calculated using TREE-PUZZLE v.5.2 [43] and PUZZLEBOOT v.1.03 (A. Roger and M. Holder, http://www.tree-puzzle.de. The models used in TREE-PUZZLE/BUZZLEBOOT to calculate the maximum likelihood distances were the same as those determined by ModelGenerator.…”

Section: Methodsmentioning

confidence: 99%

Evidence for acquisition of virulence effectors in pathogenic chytrids

et al. 2011

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BackgroundThe decline in amphibian populations across the world is frequently linked to the infection of the chytrid fungus Batrachochytrium dendrobatidis (Bd). This is particularly perplexing because Bd was only recently discovered in 1999 and no chytrid fungus had previously been identified as a vertebrate pathogen.ResultsIn this study, we show that two large families of known virulence effector genes, crinkler (CRN) proteins and serine peptidases, were acquired by Bd from oomycete pathogens and bacteria, respectively. These two families have been duplicated after their acquisition by Bd. Additional selection analyses indicate that both families evolved under strong positive selection, suggesting that they are involved in the adaptation of Bd to its hosts.ConclusionsWe propose that the acquisition of virulence effectors, in combination with habitat disruption and climate change, may have driven the Bd epidemics and the decline in amphibian populations. This finding provides a starting point for biochemical investigations of chytridiomycosis.

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“…For the phylogenetic analyses, 680 bp of cox1 and 401 bp of 16S rRNA fragments were used. To infer phylogenetic relationships, neighbour-joining algorithm (NJ), maximum parsimony analysis (MP) with MEGA 4.0 (Tamura et al, 2007) and maximum likelihood method (ML) with TREE-PUZZLE 5.1 (Schmidt et al, 2002) were performed. TamuraNei distance (D TrN ; Tamura and Nei, 1993) was used for the NJ trees.…”

Section: Methodsmentioning

confidence: 99%

Low genetic diversity in Polish populations of sibling ant species: Lasius niger (L.) and Lasius platythorax Seifert (Hymenoptera, Formicidae)

Wysocka

Krzysztofiak²,

Krzysztofiak³

et al. 2010

Insect. Soc.

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We present preliminary data on mitochondrial DNA diversity within and among populations of the ants Lasius niger and Lasius platythorax in Poland. Phylogenetic analysis based on the mitochondrial DNA markers: cytochrome c oxidase subunit I (cox1) and 16S ribosomal RNA (16S rRNA) confirms the species status of L. niger and L. platythorax. Intraspecific variability is low in both species, which might be a result of severe bottlenecks and rapid postglacial expansion into Central Europe.

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TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing

Cited by 2,362 publications

References 20 publications

Genome sequence of the recombinant protein production host Pichia pastoris

Genome sequence of the recombinant protein production host Pichia pastoris

Evidence for acquisition of virulence effectors in pathogenic chytrids

Low genetic diversity in Polish populations of sibling ant species: Lasius niger (L.) and Lasius platythorax Seifert (Hymenoptera, Formicidae)

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