QuickTree: Building huge Neighbour-Joining trees of protein sequences

The Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK.
Bioinformatics (Impact Factor: 4.98). 12/2002; 18(11):1546-7. DOI: 10.1093/bioinformatics/18.11.1546
Source: PubMed


We have written a fast implementation of the popular Neighbor-Joining tree building algorithm. QuickTree allows the reconstruction of phylogenies for very large protein families (including the largest Pfam alignment containing 27000 HIV GP120 glycoprotein sequences) that would be infeasible using other popular methods. Availability: The source-code for QuickTree , written in ANSI~C, is freely available via the world wide web at Contact: * To whom correspondence should be addressed. </fn

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Available from: Alex Bateman, Jun 06, 2014
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    • "genetic trees using the neighbor-joining (NJ) method as implemented in QuickTree (Howe et al. 2002). "
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    ABSTRACT: Here we used both microsatellites and mtCR (mitochondrial DNA control region) sequences as genetic markers to examine the genetic diversity and population structure of Penaeus monodon shrimp from six Indonesian regions. The microsatellite data showed that shrimp from the Indian and the Pacific Ocean were genetically distinct from each other. It has been reported previously that P. monodon mtCR sequences from the Indo-Pacific group into two major paral-ogous clades of unclear origin. Here we show that the population structure inferred from mtCR sequences matches the microsatellite-based population structure for one of these clades. This is consistent with the notion that this mtCR clade shares evolutionary history with nuclear DNA and may thus represent nuclear mitochondrial pseudogenes (Numts).
    Ecology and Evolution 08/2015; DOI:10.1002/ece3.1616 · 2.32 Impact Factor
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    • "Multiple sequence alignment (MSA) for each family was built using ClustalW. For phylogenetic analysis, bootstrapped trees were built and visualized using QuickTree (Howe et al. 2002) tool of PHYLIP package and iTOL, respectively. The phylogenetic trees can be accessed using the URL "
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    ABSTRACT: Bacterial phosphothreonine lyases catalyze a novel post-translational modification involving formation of dehydrobutyrine/dehyroalanine by β elimination of the phosphate group of phosphothreonine or phosphoserine residues in their substrate proteins. Though there is experimental evidence for presence of dehydro amino acids in human proteins, no eukaryotic homologs of these lyases have been identified as of today. A comprehensive genome wide search for identifying phosphothreonine lyase homologs in eukaryotes was carried out. Our fold based search revealed structural and catalytic site similarity between bacterial phosphothreonine lyases and BLES03, a human protein with unknown function. Ligand induced conformational changes similar to bacterial phosphothreonine lyases, and movement of crucial arginines in the loop region to the catalytic pocket upon binding of phosphothreonine containing peptides was seen during docking and molecular dynamics studies. Genome wide search for BLES03 homologs using sensitive profile based methods revealed their presence not only in eukaryotic classes like chordata and fungi, but also in bacterial and archaebacterial classes. The synteny of these archaebacterial BLES03 like proteins was remarkably similar to that of type IV lantibiotic synthetases which harbor LanL like phosphothreonine lyase domains. Hence, context based analysis reinforced our earlier sequence/structure based prediction of phosphothreonine lyase catalytic function for BLES03. Our in silico analysis has revealed that BLES03 like proteins with previously unknown function are novel eukaryotic phosphothreonine lyases involved in biosynthesis of dehydro amino acids, while their bacterial and archaebacterial counterparts might be involved in biosynthesis of natural products similar to lantibiotics.
    Genome Biology and Evolution 07/2014; 6(8). DOI:10.1093/gbe/evu161 · 4.23 Impact Factor
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    • "Thus, we used a method to filter the potential non-targets based on the preliminary phylogenetic analysis of all sequences matching the HMM profile. Firstly, full sequence dataset were aligned by ClustalW-MPI (Li, 2003), and subjected to neighbor-joining tree reconstruction by Quick- Tree (Howe et al., 2002). Secondly, all protein sequences were clustered based on the pairwise distance (60.3). "
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    ABSTRACT: Despite intense scrutiny from researchers in the fields of biochemistry and metabolism, our understanding of the evolutionary history of the key anabolic shikimate pathway remains limited. To shed light on the early evolutionary events leading to the assembly of the pathway, we investigated the distributions, domain architectures and phylogenies of component enzymes using a bioinformatic procedure based on Hidden Markov Model profiles. The aro genes for the canonical shikimate pathway had most wider distribution in prokaryotes; and the variant pathway coordinated by 2-amino-3,7- dideoxy-D-threo-hept-6-ulosonic acid (ADH) synthase and type II 3-dehydroquinate (DHQ) synthase could be identified in most of archaeal species. In addition, the ancient bidirectional horizontal gene transfer events had happened between two prokaryotic domains: Bacteria and Archaea. Besides 3- deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase, the phylogenetically distinct subfamilies of 5-enolpyruvylshikimate 3-phosphate (EPSP) synthase and chorismate synthase had ever emerged in the evolutionary history of shikimate pathway. These findings provide new insight into the early evolution of the shikimate pathway and advance our understanding of the evolution of metabolic pathways.
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