Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments.

No abstract is available for this paper.

• Publication year

  2007

• Venue

  Systematic Biology

• Publication date

  2007-08-01

• Fields of study

  Biology, Medicine, Computer Science

• Identifiers
  DOI 10.1080/10635150701472164PMID 17654362
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Progressive sequence alignment as a prerequisitetto correct phylogenetic trees

  2007cited by this paper
• Analysis and Comparison of Benchmarks for Multiple Sequence Alignment

  2006cited by this paper
• Multiple sequence alignment.

  2006cited by this paper
• Phylogenomics: the beginning of incongruence?

  2006influential reference
• The accuracy of several multiple sequence alignment programs for proteins

  2006cited by this paper
• Nematode small subunit phylogeny correlates with alignment parameters.

  2006cited by this paper
• MAFFT version 5: improvement in accuracy of multiple sequence alignment

  2005cited by this paper
• Bayesian coestimation of phylogeny and sequence alignment

  2005cited by this paper
• ProbCons: Probabilistic consistency-based multiple sequence alignment.

  2005influential reference
• Mind the gaps: progress in progressive alignment.

  2005cited by this paper
• Simultaneous statistical multiple alignment and phylogeny reconstruction.

  2005cited by this paper
• Kalign – an accurate and fast multiple sequence alignment algorithm

  2005cited by this paper
• Multiple Sequence Alignment

  2005cited by this paper
• BAliBASE 3.0: Latest developments of the multiple sequence alignment benchmark

  2005cited by this paper
• Phylogenomics and the reconstruction of the tree of life

  2005cited by this paper
• Joint Bayesian estimation of alignment and phylogeny.

  2005cited by this paper
• The information content of an ambiguously alignable region, a case study of the trnL intron from the Rhamnaceae

  2004influential reference
• MUSCLE: multiple sequence alignment with high accuracy and high throughput.

  2004cited by this paper
• A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood.

  2003cited by this paper
• GapCoder automates the use of indel characters in phylogenetic analysis

  2003cited by this paper
• 18S ribosomal RNA and tetrapod phylogeny.

  2003cited by this paper
• The COG database: an updated version includes eukaryotes

  2003cited by this paper
• MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform.

  2002influential reference
• Stretch Coding and Block Coding: Two New Strategies to Represent Questionably Aligned DNA Sequences

  2002cited by this paper
• The Bioperl toolkit: Perl modules for the life sciences.

  2002cited by this paper
• PAL: an object-oriented programming library for molecular evolution and phylogenetics

  2001cited by this paper
• Homology and the Optimization of DNA Sequence Data

  2001cited by this paper
• SOAP, cleaning multiple alignments from unstable blocks

  2001cited by this paper
• Unalignable sequences and molecular evolution

  2001influential reference
• Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis.

  2000influential reference
• Integrating ambiguously aligned regions of DNA sequences in phylogenetic analyses without violating positional homology.

  2000cited by this paper
• [General method].

  2000cited by this paper
• T-Coffee: A novel method for fast and accurate multiple sequence alignment.

  2000cited by this paper
• Phylogenetic inference from conserved sites alignments.

  1999cited by this paper
• Rose: generating sequence families

  1998cited by this paper
• The mitochondrial genome of the hemichordate Balanoglossus carnosus and the evolution of deuterostome mitochondria.

  1998cited by this paper
• Codon reassignment and amino acid composition in hemichordate mitochondria.

  1998cited by this paper
• On the Best Evolutionary Rate for Phylogenetic Analysis

  1998cited by this paper
• How good are deep phylogenetic trees?

  1998cited by this paper
• On the best evolutionary rate for phylogenetic analysis.

  1998cited by this paper
• Effects of nucleotide sequence alignment on phylogeny estimation: a case study of 18S rDNAs of apicomplexa.

  1997cited by this paper
• CONRAD: a method for identification of variable and conserved regions within proteins by scale-space filtering

  1996cited by this paper
• Quartet Puzzling: A Quartet Maximum-Likelihood Method for Reconstructing Tree Topologies

  1996cited by this paper
• Use of rRNA secondary structure in phylogenetic studies to identify homologous positions: an example of alignment and data presentation from the frogs.

  1995cited by this paper
• Inadequate Support for an Evolutionary Link between the Metazoa and the Fungi

  1994cited by this paper
• CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.

  1994influential reference
• Lessons from an evolving rRNA: 16S and 23S rRNA structures from a comparative perspective.

  1994cited by this paper
• Protein family classification based on searching a database of blocks.

  1994cited by this paper
• Alignment-ambiguous nucleotide sites and the exclusion of systematic data.

  1993cited by this paper
• The rapid generation of mutation data matrices from protein sequences

  1992cited by this paper
• A statistical method for detecting regions with different evolutionary dynamics in multialigned sequences.

  1992cited by this paper
• The order of sequence alignment can bias the selection of tree topology.

  1991cited by this paper
• Comparison of phylogenetic trees

  1981cited by this paper
• A model of evolutionary change in protein

  1978cited by this paper
• Chapter 22: A model of evolutionary change in proteins

  1978cited by this paper
• A general method applicable to the search for similarities in the amino acid sequence of two proteins.

  1970cited by this paper

• Chromosome-level genome assembly of the deep-sea solemyid bivalve Acharax haimaensis.

  2026cites this paper
• INSIG1 parallel substitution drives lipid/sterol metabolic plasticity mediating desert adaptation in ungulates

  2026cites this paper
• Nutritional specialization and social evolution in woodroaches and termites.

  2026cites this paper
• Gondwanan Origin of Bark and Ambrosia Beetles and Their Rapid Worldwide Diversification During the Cretaceous

  2026cites this paper
• The Complete Mitochondrial Genome of Eucrate alcocki (Decapoda: Brachyura: Euryplacidae) Provides New Insights Into Heterotrematan Crab Phylogeny.

  2026cites this paper
• Core Transcriptional Plasticity Pave the Way for Fish to Succeed in a High‐CO2 World

  2026cites this paper
• Harnessing Chaetomium globosum for fungal biocontrol: pigmentation and metabolic responses in Bipolaris sorokiniana

  2026cites this paper
• Sedum zhenghaianum (Crassulaceae), a new species from Zhejiang and Jiangxi, East China

  2026cites this paper
• Integrating morphology and phylogenetics reveals new species, records, and provides an updated checklist of Trichiaceae in China.

  2026cites this paper
• Medicinal Plant Crotalaria pallida: Molecular Sequencing and Characterization of its Seed Extract

  2026cites this paper
• Evolutionary mobility and genetic dynamics of MORFFO genes: shuttling among ancient plant lineages.

  2026cites this paper
• COI based phylogeny and morphological characterization of a Brazilian population of Lambornella trichoglossa (Ciliophora: Tetrahymenidae)

  2026cites this paper
• Why are so few island bryophytes endemic?

  2026cites this paper
• Comparative insights into molecular pathways influencing germline development in early‐divergent angiosperms

  2026cites this paper
• Nucleophaga amutiana, sp. nov.-a novel intranuclear parasite of amoebae from the Far East of Russia expands the diversity and biogeography of microsporidia-like organisms.

  2026cites this paper
• Deep-Sea Bamboo Corals: New Jasonisis Species from Indian and Atlantic Ridges and Pan-Oceanic Genetic Connectivity of Tridentisis candelabrum

  2026cites this paper
• Hericium americanum var. roseum—a new North American taxon

  2026cites this paper
• Essential function reflected in the phylodynamics of a multigene family – the pir genes of malaria parasites

  2026cites this paper
• Angiopteris weimingii (Marattiaceae): a new endangered fern species from southern Yunnan, China, revealed by morphology and phylogeny

  2026cites this paper
• The complete plastome and phylogenetic analysis of Zingiber ottensii Valeton

  2026cites this paper
• Living in each other's pockets: insights into the life cycle of Tremella caloplacae s. l.

  2026cites this paper
• Comparative mitogenomics and phylogenetic implications of Dawkinsia apsara and Dawkinsia denisonii (Cypriniformes, Cyprinidae).

  2026cites this paper
• Benzene contamination from operating petrochemical enterprises alters in-situ microbial communities and metabolic potential in groundwater

  2026cites this paper
• The ambrosial mycobiota of Treptoplatypus oxyurus (Coleoptera, Platypodidae): a unique island of fungal diversity revealing Wilhelmdebeerea oxyuri gen. et sp. nov. (Ophiostomatales), and two new yeast species Blastobotrys sasensis sp. nov., and Sugiyamaella casensis sp. nov. (Dipodascales).

  2026cites this paper
• Viromics in flat mites from Hawaii shows abundant arrays of viruses, expands the evolutionary origin of plant viruses, and provides a surveillance tool for Brevipalpus-transmitted viruses

  2026cites this paper
• Establishment of a stable monoculture system for Entodinium furca monolobum and isolation of Escherichia spp. as growth-promoting bacteria.

  2026cites this paper
• Autotrophic methylotrophy with no methanol dehydrogenase (MDH) in a strain of fluorescent Pseudomonas

  2026cites this paper
• Phytophthora capsici carries and differentially expresses genes for the RNA interference pathway

  2026cites this paper
• Phylogenetic relationships and modeling distributions of the monotypic genus Dolichopetalum (Apocynaceae): Implications for conservation of unique biodiversity in Asian subtropical karst areas

  2026cites this paper
• Exploring bioactive potential of epiphytic and endophytic bacteria from Gelidium pusillum: a study on secondary metabolites and therapeutic applications

  2026influential citation
• The first complete mitochondrial genome characterization of Lutjanus fulvus (Perciformes: Lutjanidae) and phylogenetic analysis within the Lutjanidae family

  2026cites this paper
• Decoding the first mitogenomes of Polycelis (Platyhelminthes, Tricladida, Planariidae): genomic architecture, evolutionary dynamics, and phylogenomic implication

  2026cites this paper
• Complete mitogenomes of two species of Cephenemyia and Pharyngomyia picta, and a comparison with other Oestrinae

  2026cites this paper
• The complete chloroplast genome of Calystegia pubescens ‘Anestia’ Hara 1957 (Convolvulaceae), an endemic species in Asia

  2026cites this paper
• Phylogenomics and biogeography of the cleptoparasitic bee genus Triepeolus Robertson (Hymenoptera: Apidae), with a revised subgeneric classification of Triepeolus and its sister genus, Epeolus Latreille

  2026cites this paper
• Three new species of Buellia s.l. from the Qinghai-Tibetan Plateau represent a new lineage, the pruinocalcarea-group.

  2026cites this paper
• Mitogenomic insights into the speciation and evolutionary history of the stag beetle genus Hexarthrius (Coleoptera: Lucanidae)

  2026cites this paper
• Pinopsin Regulates Melatonin Production and Daily Locomotor Activity: Functional Insights From Gene‐Edited Xenopus Tadpoles

  2026cites this paper
• Genomics Insights Into High‐Latitude Adaptation of Tibetan Macaques

  2026cites this paper
• Genomes of N2-fixing endosymbionts of unicellular eukaryotes and host-independence

  2026cites this paper
• Mitogenomes of Seven Malaysian Marine Gastropods Recovered Using Genome Skimming

  2026cites this paper
• Phylogenetic evidence reveals the classification and evolutionary history of endemic cavefish in China

  2026influential citation
• Multipartite mitochondrial genome evolution in Halophila seagrasses: repeat-driven structural plasticity and selection signatures of marine adaptation.

  2026cites this paper
• Scuticeratina: A new subgenus of small carpenter bees (Hymenoptera, Apidae, Xylocopinae) from Indomalaya.

  2026influential citation
• The complete mitochondrial genome of Atheraster arandae (Asteroidea: Valvatida: Goniasteridae) from the western Pacific

  2026influential citation
• DrosGB: An integrated multi-omics database for comparative genomics and functional annotation of 35 Drosophila species

  2026cites this paper
• Comparative mitochondrial genomics suggests lack of deep host-associated divergence in Pulex irritans (Arthropoda: Insecta): A one health perspective.

  2026cites this paper
• Descriptions of Two New Species of Encarsia (Hymenoptera: Aphelinidae) and Mitochondrial Genome Analysis of Three Species of the Genus †

  2026cites this paper
• Lyngbyabellin Q, an Antimalarial Cyclic Peptide, and Its Acyclic Analog from a Cyanobacterial Biomat Dominated by Moorena sp.

  2026cites this paper
• Detection and localization of a new Wolbachia from supergroup W in Oppiella nova (Acari: Oribatida: Oppiidae) with potential impacts on host life-history traits.

  2026cites this paper
• Aberrant GPX4 processing reveals its critical roles in maintaining ROS homeostasis in Citrus

  2026cites this paper
• Zoological transmission of encephalomyocarditis virus in the United States: Virus evolution, host ecology, and capsid antigenicity derived from an outbreak.

  2026cites this paper
• Characterization and geographical variation of the mitochondrial genome in the Azure-winged Magpie (Cyanopica cyanus).

  2026cites this paper
• A chromosome level genome, as well as transcriptomes and metabolomes, insights into genome evolution and the biosynthesis of kaempferol and kaempferol derivatives in Impatiens balsamina (Balsaminaceae).

  2026cites this paper
• Ultraconserved elements support a new tribal‐level classification for Australasian endemic dung beetles (Coleoptera: Scarabaeidae: Scarabaeinae)

  2026cites this paper
• Two New Species of the Genus Caryanda Stål, 1878 (Orthoptera: Acrididae) from Yunnan, China Identified Based on Morphological and Molecular Data.

  2026cites this paper
• Phylogenetic Relationships of Plant Bugs Based on Mitochondrial Genomes (Heteroptera: Miridae)

  2026cites this paper
• Mitochondrial genome evaluation and implications for phylogenetic relationships of Haemadipsa hainana song, Zhang and Tan 1977 (Arhynchobdellida: Haemadipsidae)

  2026cites this paper
• The first mitochondrial genome sequence and phylogenetic analysis of Clinostomum piscidium (Platyhelminthes: Clinostomidae): a first representative from India.

  2026cites this paper
• Mitochondrial genome analysis and molecular identification of two Culex tritaeniorhynchus (Diptera: Culicidae) clades from the Republic of Korea.

  2026cites this paper
• Morphological and Molecular Evidence Revealed New Species in Mactra antiquata Sensu Lato

  2026cites this paper
• Genomic evidence for ancient introgression and paleogeoclimate co‐driving diversification in cavefish adaptive radiation

  2026influential citation
• Generalists link peaks in the shifting adaptive landscape of Australia’s dragon lizards

  2026cites this paper
• Assessing fish diversity and community keystone species in urbanized estuarine-coastal areas using eDNA metabarcoding and network analysis: A coastal management perspective

  2026cites this paper
• Biosynthesis of Pseudomonas aeruginosa mediated silver nanoparticles for remediation of crude oil contaminated water

  2026cites this paper
• Demographic history and identification of threats under climate and anthropogenic activity provide insights into conservation for Cypripedium palangshanense

  2026cites this paper
• The complete mitochondrial genome of Sindiplozoon coreius: genome structure description, comparative analysis, and phylogenetic implications

  2026cites this paper
• First record of Notocrinus (Echinodermata: Crinoidea) in the Atlantic: a new species challenges the limits of the Antarctic genus

  2026cites this paper
• Liliumbrunneum (Liliaceae): a newly discovered species in north-western Yunnan, China

  2025cites this paper
• Genomic insights into host–Endozoicomonadaceae cophylogeny

  2025cites this paper
• Two new species of freshwater planarian from Hainan Island and Leizhou Peninsula, southern China (Platyhelminthes, Tricladida, Dugesiidae)

  2025cites this paper
• The genus Artomyces (Auriscalpiaceae, Basidiomycota) from the Gaoligong Mountains and adjacent areas, southwestern China

  2025cites this paper
• Termites became the dominant decomposers of the tropics after two diversification pulses

  2025cites this paper
• Sealgamide: An Antitrypanosomal Lipopeptide Isolated from a Marine Okeania sp. Cyanobacterium.

  2025cites this paper
• Chromosome-scale genome assembly of Zoysia japonica uncovers cold tolerance candidate genes

  2025influential citation
• High Diversity and Prevalence of Rickettsial Agents in Rhipicephalus microplus Ticks from Livestock in Karst Landscapes of Southwest China

  2025cites this paper
• Renal myxosporidiosis by an unknown Bivalvulidan myxozoan parasite in Murray River turtles (Emydura macquarii) in Australia

  2025cites this paper
• Reclassification of eleven corticioid basidiomycetes with nine typifications.

  2025cites this paper
• Primulinananlingensis (Gesneriaceae), a new species from the Limestone Karst of Guangdong, China

  2025influential citation
• Hedopeptolide, a NO Production Inhibitor from the Marine Cyanobacterium Okeania sp.

  2025cites this paper
• Studies on the Epipolythiodioxopiperazine Alkaloid Verticillin D: Scaled Production, Streamlined Purification, and Absolute Configuration.

  2025cites this paper
• The complete chloroplast genome of Polygala tatarinowii (Polygalaceae)

  2025cites this paper
• The mitogenome of Triatoma brasiliensis brasiliensis (Hemiptera: Reduviidae), the main Chagas disease vector in the semi-arid region of northeastern Brazil

  2025cites this paper
• A Multilevel Biodiversity Approach of the Hermit Crabs in the Iberian Peninsula and Ultraperipheral Territories

  2025cites this paper
• The complete mitochondrial genome analysis of Haemaphysalis hystricis Supino, 1897 (Ixodida: Ixodidae) and its phylogenetic implications

  2025cites this paper
• Comparative Mitogenomes and Phylogenetic Analyses of Coccinellidae (Coleoptera: Coccinelloidea)

  2025cites this paper
• Molecular characterization of Ehrlichia canis in dogs from Brazil: a worldwide perspective.

  2025cites this paper
• Integrative omics reveals mechanisms of biosynthesis and regulation of floral scent in Cymbidium tracyanum

  2025cites this paper
• Exploring the diversity of Brachonella: Morphological and molecular analysis with the discovery of a new species, Brachonella tenuicauda nov. spec. (Ciliophora, Armophorea, Metopida).

  2025cites this paper
• The mitochondrial genome of Melipona fasciculata and Melipona quadrifasciata : molecular evolution dynamics in stingless bees (Hymenoptera: Meliponini) mitogenomes

  2025cites this paper
• Low Wolbachia incidence in Bactrocera and Zeugodacus species from Thailand and genome analysis of Wolbachia associated with Zeugodacus apicalis

  2025cites this paper
• Time series comparative genomics analysis reveals the adaptive evolution of caproic acid-producing bacteria to the long-term liquor brewing environment

  2025cites this paper
• Multiomic analysis reveals that the flavonoid biosynthesis pathway is associated with cold tolerance in Heracleum moellendorffii Hance

  2025cites this paper
• Hospesneotomae n. gen. of the Triatomini tribe presents a turnaround in the taxonomy of the Triatoma protracta species complex

  2025influential citation
• Section-level genome sequencing and comparative genomics of Aspergillus sections Cavernicolus and Usti.

  2025cites this paper
• Disconnecting trapdoors: Phylogenomic analyses reveal evolutionary contrasts in trapdoor spiders with intercontinental distribution (Idiopidae, Idiopinae).

  2025cites this paper
• An Extensive Survey of Vertebrate-specific, Nonvisual Opsins Identifies a Novel Subfamily, Q113-Bistable Opsin

  2025cites this paper
• Multiomics analysis provides insights into musk secretion in muskrat and musk deer

  2025cites this paper
• The complete mitochondrial genome and phylogenetic analysis of Lotus corniculatus (Fabaceae, Papilionoideae)

  2025cites this paper
• Parallel floral evolution of Lilium species pollinated by pierid butterflies

  2025cites this paper