Repeatability of clades as a criterion of reliability: a case study for molecular phylogeny of Acanthomorpha (Teleostei) with larger number of taxa.

doi:10.1016/S1055-7903(02)00371-8

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Repeatability of clades as a criterion of reliability: a case study for molecular phylogeny of Acanthomorpha (Teleostei) with larger number of taxa.

Journal Article•DOI•

Repeatability of clades as a criterion of reliability: a case study for molecular phylogeny of Acanthomorpha (Teleostei) with larger number of taxa.

Wei-Jen Chen¹, Céline Bonillo¹, Guillaume Lecointre¹•Institutions (1)

Centre national de la recherche scientifique¹

01 Feb 2003-Molecular Phylogenetics and Evolution (Academic Press)-Vol. 26, Iss: 2, pp 262-288

TL;DR: This study represents the most extensive taxonomic sampling effort to date to collect new molecular characters for phylogenetic analysis of acanthomorph fishes, with new and reliable clades emerging from this study of the acanthomorphic radiation.

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About: This article is published in Molecular Phylogenetics and Evolution.The article was published on 2003-02-01. It has received 350 citations till now. The article focuses on the topics: Acanthomorpha & Zoarcoidei.

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Journal Article•DOI•

The tree of life and a new classification of bony fishes.

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Ricardo Betancur-R.¹, Richard E. Broughton², Edward O. Wiley³, Kent E. Carpenter⁴, J. Andrés López⁵, Chenhong Li⁶, Nancy I. Holcroft⁷, Dahiana Arcila¹, Millicent D. Sanciangco⁸, James C. Cureton², Feifei Zhang, Thaddaeus John Buser, Matthew A. Campbell⁵, Jesús A. Ballesteros¹, Adela Roa-Varon, Stuart C. Willis⁹, W. Calvin Borden¹⁰, Thaine W. Rowley¹¹, Paulette C. Reneau¹², Daniel J. Hough², Guoqing Lu, Terry Grande, Gloria Arratia, Guillermo Ortí¹ - Show less +20 more•Institutions (12)

George Washington University¹, University of Oklahoma², University of Kansas³, International Union for Conservation of Nature and Natural Resources⁴, University of Alaska Fairbanks⁵, Shanghai Ocean University⁶, Johnson County Community College⁷, Old Dominion University⁸, University of Nebraska–Lincoln⁹, Loyola University Chicago¹⁰, University of Nebraska Omaha¹¹, Florida A&M University¹²

18 Apr 2013-PLOS Currents

TL;DR: A comprehensive molecular phylogeny for bony fishes that includes representatives of all major lineages and the order Perciformes, considered by many a polyphyletic taxonomic waste basket, is defined for the first time as a monophyletic group in the global phylogeny.

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Abstract: The tree of life of fishes is in a state of flux because we still lack a comprehensive phylogeny that includes all major groups. The situation is most critical for a large clade of spiny-finned fishes, traditionally referred to as percomorphs, whose uncertain relationships have plagued ichthyologists for over a century. Most of what we know about the higher-level relationships among fish lineages has been based on morphology, but rapid influx of molecular studies is changing many established systematic concepts. We report a comprehensive molecular phylogeny for bony fishes that includes representatives of all major lineages. DNA sequence data for 21 molecular markers (one mitochondrial and 20 nuclear genes) were collected for 1410 bony fish taxa, plus four tetrapod species and two chondrichthyan outgroups (total 1416 terminals). Bony fish diversity is represented by 1093 genera, 369 families, and all traditionally recognized orders. The maximum likelihood tree provides unprecedented resolution and high bootstrap support for most backbone nodes, defining for the first time a global phylogeny of fishes. The general structure of the tree is in agreement with expectations from previous morphological and molecular studies, but significant new clades arise. Most interestingly, the high degree of uncertainty among percomorphs is now resolved into nine well-supported supraordinal groups. The order Perciformes, considered by many a polyphyletic taxonomic waste basket, is defined for the first time as a monophyletic group in the global phylogeny. A new classification that reflects our phylogenetic hypothesis is proposed to facilitate communication about the newly found structure of the tree of life of fishes. Finally, the molecular phylogeny is calibrated using 60 fossil constraints to produce a comprehensive time tree. The new time-calibrated phylogeny will provide the basis for and stimulate new comparative studies to better understand the evolution of the amazing diversity of fishes.

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740 citations

Journal Article•DOI•

Phylogenetic classification of bony fishes.

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Ricardo Betancur-R.¹, Ricardo Betancur-R.², Edward O. Wiley³, Edward O. Wiley⁴, Gloria Arratia⁴, Arturo Acero⁵, Nicolas Bailly, Masaki Miya⁶, Guillaume Lecointre, Guillermo Ortí⁷, Guillermo Ortí¹ - Show less +7 more•Institutions (7)

National Museum of Natural History¹, University of Puerto Rico², Sam Houston State University³, University of Kansas⁴, National University of Colombia⁵, American Museum of Natural History⁶, George Washington University⁷

06 Jul 2017-BMC Evolutionary Biology

TL;DR: This version of the phylogenetic classification of bony fishes is substantially improved, providing resolution for more taxa than previous versions, based on more densely sampled phylogenetic trees.

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Abstract: Fish classifications, as those of most other taxonomic groups, are being transformed drastically as new molecular phylogenies provide support for natural groups that were unanticipated by previous studies. A brief review of the main criteria used by ichthyologists to define their classifications during the last 50 years, however, reveals slow progress towards using an explicit phylogenetic framework. Instead, the trend has been to rely, in varying degrees, on deep-rooted anatomical concepts and authority, often mixing taxa with explicit phylogenetic support with arbitrary groupings. Two leading sources in ichthyology frequently used for fish classifications (JS Nelson’s volumes of Fishes of the World and W. Eschmeyer’s Catalog of Fishes) fail to adopt a global phylogenetic framework despite much recent progress made towards the resolution of the fish Tree of Life. The first explicit phylogenetic classification of bony fishes was published in 2013, based on a comprehensive molecular phylogeny ( www.deepfin.org ). We here update the first version of that classification by incorporating the most recent phylogenetic results. The updated classification presented here is based on phylogenies inferred using molecular and genomic data for nearly 2000 fishes. A total of 72 orders (and 79 suborders) are recognized in this version, compared with 66 orders in version 1. The phylogeny resolves placement of 410 families, or ~80% of the total of 514 families of bony fishes currently recognized. The ordinal status of 30 percomorph families included in this study, however, remains uncertain (incertae sedis in the series Carangaria, Ovalentaria, or Eupercaria). Comments to support taxonomic decisions and comparisons with conflicting taxonomic groups proposed by others are presented. We also highlight cases were morphological support exist for the groups being classified. This version of the phylogenetic classification of bony fishes is substantially improved, providing resolution for more taxa than previous versions, based on more densely sampled phylogenetic trees. The classification presented in this study represents, unlike any other, the most up-to-date hypothesis of the Tree of Life of fishes.

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622 citations

Journal Article•DOI•

Taxon sampling and the accuracy of phylogenetic analyses

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Tracy A. Heath, Shannon M. Hedtke, David M. Hillis

23 Apr 2008-Journal of Systematics and Evolution

TL;DR: Thorough taxon sampling is one of the most practical ways to improve the accuracy of phylogenetic estimates, as well as the accuracyof biological inferences that are based on these phylogenetic trees.

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Abstract: Appropriate and extensive taxon sampling is one of the most important determinants of accurate phylogenetic estimation. In addition, accuracy of inferences about evolutionary processes obtained from phyloge- netic analyses is improved significantly by thorough taxon sampling efforts. Many recent efforts to improve phylogenetic estimates have focused instead on increasing sequence length or the number of overall characters in the analysis, and this often does have a beneficial effect on the accuracy of phylogenetic analyses. However, phylogenetic analyses of few taxa (but each represented by many characters) can be subject to strong systematic biases, which in turn produce high measures of repeatability (such as bootstrap proportions) in support of incor- rect or misleading phylogenetic results. Thus, it is important for phylogeneticists to consider both the sampling of taxa, as well as the sampling of characters, in designing phylogenetic studies. Taxon sampling also improves estimates of evolutionary parameters derived from phylogenetic trees, and is thus important for improved applica- tions of phylogenetic analyses. Analysis of sensitivity to taxon inclusion, the possible effects of long-branch attraction, and sensitivity of parameter estimation for model-based methods should be a part of any careful and thorough phylogenetic analysis. Furthermore, recent improvements in phylogenetic algorithms and in computa- tional power have removed many constraints on analyzing large, thoroughly sampled data sets. Thorough taxon sampling is thus one of the most practical ways to improve the accuracy of phylogenetic estimates, as well as the accuracy of biological inferences that are based on these phylogenetic trees.

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527 citations

Cites background from "Repeatability of clades as a criter..."

...…of phylogenetic analyses often attribute problematic reconstruction and low resolution to inadequate taxon sampling (e.g., Bremer et al., 1999; Johnson, 2001; Lin et al., 2002; Braun & Kimball, 2002; Chen et al., 2003; Freudenstein et al., 2003; Sorenson et al., 2003; Albrecht et al., 2007)....
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...particularly those based on traditional morphological taxonomy versus molecular analyses—may be the first signal that LBA may be present in the data set (Lin et al., 2002; Chen et al., 2003)....
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...Disagreement among independent data sets— particularly those based on traditional morphological taxonomy versus molecular analyses—may be the first signal that LBA may be present in the data set (Lin et al., 2002; Chen et al., 2003)....
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Journal Article•DOI•

The nature of the diversity of Antarctic fishes

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Joseph T. Eastman¹•Institutions (1)

Ohio University¹

01 Jan 2005-Polar Biology

TL;DR: The species diversity of the Antarctic fish fauna changed notably during the ≈40 million years from the Eocene to the present, and in some notothenioid clades phyletic diversification was accompanied by considerable morphological and ecological diversification.

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Abstract: The species diversity of the Antarctic fish fauna changed notably during the ≈40 million years from the Eocene to the present. A taxonomically restricted and endemic modern fauna succeeded a taxonomically diverse and cosmopolitan Eocene fauna. Although the Southern Ocean is 10% of the world’s ocean, its current fish fauna consists of only 322 species, small considering the global diversity of ≈25,000–28,000 species. The fauna is “reasonably well-known” from a taxonomic perspective. This intermediate designation between “poorly known” and “well-known” indicates that new species are regularly being described. A conservative estimate of the number of undescribed species is ≈30–60; many of these may be liparids. On the Antarctic continental shelf and upper slope the fauna includes 222 species from 19 families of benthic fishes. The most speciose taxa are notothenioids, liparids and zoarcids, accounting for 88% of species diversity. Endemism for Antarctic species is also, coincidentally, 88%, at least threefold higher than in faunas from other isolated marine localities. Eight notothenioid families, including five that are primarily Antarctic, encompass a total of 44 genera and 129 species, 101 Antarctic and 28 non-Antarctic. The 101 Antarctic species make up 45% of the benthic species diversity in the Antarctic region. However, at the highest latitudes, notothenioids contribute 77% of the species diversity, 92% of the abundance and 91% of the biomass. Although species diversity is low compared to other shelf habitats, the nature of the adaptive radiation in organismal diversity among notothenioids is noteworthy in the marine realm. In some notothenioid clades phyletic diversification was accompanied by considerable morphological and ecological diversification. The exemplar is the benthic family Nototheniidae that underwent a habitat or depth related diversification centred on the alteration of buoyancy. They occupy an array of pelagic and benthopelagic habitats at various depths on the shelf and upper slope. Diversification in buoyancy is the hallmark of the nototheniid radiation and, in the absence of swim bladders, was accomplished by a combination of reduced skeletal mineralisation and lipid deposition. Although neutral buoyancy is found in only five species of nototheniids some, like Pleuragramma antarcticum, are abundant and ecologically important. Much work remains to be done in order to frame and to use phylogenetically based statistical methods to test hypotheses relating to the key features of the notothenioid radiation. To reach this analytical phase more completely resolved cladograms that include phyletically basal and non-Antarctic species are essential.

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369 citations

Cites background from "Repeatability of clades as a criter..."

...There has also been progress in narrowing down the sister group of notothenioids (Chen et al. 2003; Detta and Lecointre 2004)....
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...How do species diversity and rates of endemism for Antarctic fishes compare to those for faunas from adjacent areas of the Southern Hemisphere?...
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...Zoarcids also have a North Pacific origin, dispersed to the Southern Hemisphere during the Miocene and subsequently radiated in Antarctica where aArranged phylogenetically with sequencing according to Nelson (1994) bBased on Gon and Heemstra (1990); footnotes provide updates and additions for various groups cBalushkin and Voskoboinikova (1990) dAdditional liparids from Andriashev and Stein (1998), Matallanas (1998, 1999), Matallanas and Pequeño (2000), Chernova and Eastman (2001) and Chernova and Duhamel (2003) eAdditional zoarcids from Anderson (1991) fNotothenioids from Eastman and Eakin (2000) with subsequent additions of Antarctic species from Prirodina (2000, 2002, 2004) and La Mesa et al. (2002) they exhibit a major area of endemism (Anderson 1994)....
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...It is possible, however, that this finding is an artefact of sampling since percids are a Northern Hemisphere freshwater group and the dataset did not include sequences from marine perciforms living in the Southern Hemisphere (Chen et al. 2003)....
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...Notothenioids are the indigenous Southern Hemisphere component of the fauna that evolved in situ (Andriashev 1965) whereas the ancestors of the modern Antarctic liparids likely originated in the North Pacific and dispersed into the Antarctic via the west coast of South America, possibly during the Miocene (Andriashev 1991)....
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Journal Article•DOI•

Mitogenomic evolution and interrelationships of the Cypriniformes (Actinopterygii: Ostariophysi): the first evidence toward resolution of higher-level relationships of the world's largest freshwater fish clade based on 59 whole mitogenome sequences.

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Kenji Saitoh, Tetsuya Sado¹, Richard L. Mayden², Naoto Hanzawa³, K. Nakamura³, Mutsumi Nishida⁴, Masaki Miya¹ - Show less +3 more•Institutions (4)

American Museum of Natural History¹, Saint Louis University², Yamagata University³, University of Tokyo⁴

02 Nov 2006-Journal of Molecular Evolution

TL;DR: The present study represents the first attempt toward resolution of the higher-level relationships of the world’s largest freshwater-fish clade based on whole mitochondrial genome sequences from 53 cypriniforms plus 6 outgroups, and it is advocated that RY-coding, which takes only transversions into account, effectively removes this likely “noise” from the data set and avoids the apparent lack of signal by retaining all available positions in the dataSet.

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Abstract: Fishes of the order Cypriniformes are almost completely restricted to freshwater bodies and number > 3400 species placed in 5 families, each with poorly defined subfamilies and/or tribes. The present study represents the first attempt toward resolution of the higher-level relationships of the world's largest freshwater-fish clade based on whole mitochondrial (mt) genome sequences from 53 cypriniforms (including 46 newly determined sequences) plus 6 outgroups. Unambiguously aligned, concatenated mt genome sequences (14,563 bp) were divided into 5 partitions (first, second, and third codon positions of the protein-coding genes, rRNA genes, and tRNA genes), and partitioned Bayesian analyses were conducted, with protein-coding genes being treated in 3 different manners (all positions included; third codon positions converted into purine [R] and pyrimidine [Y] [RY-coding]; third codon positions excluded). The resultant phylogenies strongly supported monophyly of the Cypriniformes as well as that of the families Cyprinidae, Catostomidae, and a clade comprising Balitoridae + Cobitidae, with the 2 latter loach families being reciprocally paraphyletic. Although all of the data sets yielded nearly identical tree topologies with regard to the shallower relationships, deeper relationships among the 4 major clades (the above 3 major clades plus Gyrinocheilidae, represented by a single species Gyrinocheilus aymonieri in this study), were incongruent depending on the data sets. Treatment of the rapidly saturated third codon-position transitions appeared to be a source of such incongruities, and we advocate that RY-coding, which takes only transversions into account, effectively removes this likely "noise" from the data set and avoids the apparent lack of signal by retaining all available positions in the data set.

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321 citations

Cites background or result from "Repeatability of clades as a criter..."

...With the exception of undoubtedly polyphyletic Perciformes (Johnson and Patterson 1993; Miya et al. 2003, 2005; Chen et al. 2003; Dettai and Lecointre 2005), Cypriniformes is the largest order of all fishes, followed by Siluriformes (catfishes), with comparable species’ diversity (approximately…...
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...With the exception of undoubtedly polyphyletic Perciformes (Johnson and Patterson 1993; Miya et al. 2003, 2005; Chen et al. 2003; Dettai and Lecointre 2005), Cypriniformes is the largest order of all fishes, followed by Siluriformes (catfishes), with comparable species’ diversity (approximately 2930 spp....
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...…Lavoué et al. 2005; Minegishi et al. 2005), and the resulting trees are highly congruent with those derived from independent nuclear markers (Lê et al. 1993; Wiley et al. 2000; Zaragueta-Bagils et al. 2002; Chen et al. 2003; López et al. 2004; Smith andWheeler 2004; Dettai and Lecointre 2005)....
[...]
...With the exception of undoubtedly polyphyletic Perciformes (Johnson and Patterson 1993; Miya et al. 2003, 2005; Chen et al. 2003; Dettai and Lecointre 2005), Cypriniformes is the largest order of all fishes, followed by Siluriformes (catfishes), with comparable species’ diversity (approximately 2930 spp.; FishBase July 2005)....
[...]
...2005), and the resulting trees are highly congruent with those derived from independent nuclear markers (Lê et al. 1993; Wiley et al. 2000; Zaragueta-Bagils et al. 2002; Chen et al. 2003; López et al. 2004; Smith andWheeler 2004; Dettai and Lecointre 2005)....
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Journal Article•DOI•

The neighbor-joining method: a new method for reconstructing phylogenetic trees.

[...]

Naruya Saitou¹, Masatoshi Nei•Institutions (1)

University of Texas Health Science Center at Houston¹

01 Jul 1987-Molecular Biology and Evolution

TL;DR: The neighbor-joining method and Sattath and Tversky's method are shown to be generally better than the other methods for reconstructing phylogenetic trees from evolutionary distance data.

...read moreread less

Abstract: A new method called the neighbor-joining method is proposed for reconstructing phylogenetic trees from evolutionary distance data. The principle of this method is to find pairs of operational taxonomic units (OTUs [= neighbors]) that minimize the total branch length at each stage of clustering of OTUs starting with a starlike tree. The branch lengths as well as the topology of a parsimonious tree can quickly be obtained by using this method. Using computer simulation, we studied the efficiency of this method in obtaining the correct unrooted tree in comparison with that of five other tree-making methods: the unweighted pair group method of analysis, Farris's method, Sattath and Tversky's method, Li's method, and Tateno et al.'s modified Farris method. The new, neighbor-joining method and Sattath and Tversky's method are shown to be generally better than the other methods.

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57,055 citations

"Repeatability of clades as a criter..." refers background or methods in this paper

...To obtain ME and ML optimal trees, a neighbor-joining tree (NJ; Saitou and Nei, 1987) was used as a starting tree for heuristic searches with TBR and NNI branch swapping under the ME and ML criteria, respectively....
[...]
...A few unusual cases of phylogenetic bias, by which ‘‘incorrect’’ models can give ‘‘correct’’ answers, have been identified in both simulation (e.g., Saitou and Nei, 1987; Takahashi and Nei, 2000; Tateno et al., 1994; Yang, 1997) and empirical studies (Posada and Crandall, 2001)....
[...]

Journal Article•DOI•

Confidence limits on phylogenies: an approach using the bootstrap.

[...]

Joseph Felsenstein¹•Institutions (1)

University of Washington¹

01 Jul 1985-Evolution

TL;DR: The recently‐developed statistical method known as the “bootstrap” can be used to place confidence intervals on phylogenies and shows significant evidence for a group if it is defined by three or more characters.

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Abstract: The recently-developed statistical method known as the "bootstrap" can be used to place confidence intervals on phylogenies. It involves resampling points from one's own data, with replacement, to create a series of bootstrap samples of the same size as the original data. Each of these is analyzed, and the variation among the resulting estimates taken to indicate the size of the error involved in making estimates from the original data. In the case of phylogenies, it is argued that the proper method of resampling is to keep all of the original species while sampling characters with replacement, under the assumption that the characters have been independently drawn by the systematist and have evolved independently. Majority-rule consensus trees can be used to construct a phylogeny showing all of the inferred monophyletic groups that occurred in a majority of the bootstrap samples. If a group shows up 95% of the time or more, the evidence for it is taken to be statistically significant. Existing computer programs can be used to analyze different bootstrap samples by using weights on the characters, the weight of a character being how many times it was drawn in bootstrap sampling. When all characters are perfectly compatible, as envisioned by Hennig, bootstrap sampling becomes unnecessary; the bootstrap method would show significant evidence for a group if it is defined by three or more characters.

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40,349 citations

"Repeatability of clades as a criter..." refers background or methods in this paper

...Bootstrap analysis was used to assess the robustness of clades (Felsenstein, 1985)....
[...]
...The most common way in systematic studies to assess ‘‘reliability’’ of phylogenetic inferences is the use of indicators of robustness, such as the Bremer (or decay) index (Bremer, 1994) and bootstrap proportions (Felsenstein, 1985)....
[...]

Journal Article•DOI•

The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools.

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Julie D. Thompson¹, Toby J. Gibson, Frederica Plewniak¹, Francois Jeanmougin¹, Desmond G. Higgins² - Show less +1 more•Institutions (2)

French Institute of Health and Medical Research¹, University College Cork²

01 Dec 1997-Nucleic Acids Research

TL;DR: ClUSTAL X is a new windows interface for the widely-used progressive multiple sequence alignment program CLUSTAL W, providing an integrated system for performing multiple sequence and profile alignments and analysing the results.

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Abstract: CLUSTAL X is a new windows interface for the widely-used progressive multiple sequence alignment program CLUSTAL W. The new system is easy to use, providing an integrated system for performing multiple sequence and profile alignments and analysing the results. CLUSTAL X displays the sequence alignment in a window on the screen. A versatile sequence colouring scheme allows the user to highlight conserved features in the alignment. Pull-down menus provide all the options required for traditional multiple sequence and profile alignment. New features include: the ability to cut-and-paste sequences to change the order of the alignment, selection of a subset of the sequences to be realigned, and selection of a sub-range of the alignment to be realigned and inserted back into the original alignment. Alignment quality analysis can be performed and low-scoring segments or exceptional residues can be highlighted. Quality analysis and realignment of selected residue ranges provide the user with a powerful tool to improve and refine difficult alignments and to trap errors in input sequences. CLUSTAL X has been compiled on SUN Solaris, IRIX5.3 on Silicon Graphics, Digital UNIX on DECstations, Microsoft Windows (32 bit) for PCs, Linux ELF for x86 PCs, and Macintosh PowerMac.

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38,522 citations

"Repeatability of clades as a criter..." refers methods in this paper

...For the 28S, 12S, and 16S rDNA fragments, preliminary alignments were achieved using CLUSTAL X (Thompson et al., 1997) with default gap penalties....
[...]

Journal Article•DOI•

MODELTEST: testing the model of DNA substitution.

[...]

David Posada¹, Keith A. Crandall•Institutions (1)

Brigham Young University¹

01 Jan 1998-Bioinformatics

TL;DR: The program MODELTEST uses log likelihood scores to establish the model of DNA evolution that best fits the data.

...read moreread less

Abstract: Summary: The program MODELTEST uses log likelihood scores to establish the model of DNA evolution that best fits the data. Availability: The MODELTEST package, including the source code and some documentation is available at http://bioag.byu.edu/zoology/crandall―lab/modeltest.html. Contact: dp47@email.byu.edu.

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20,105 citations

"Repeatability of clades as a criter..." refers methods in this paper

...06 (Posada and Crandall, 1998), were employed to choose models for ML and ME analyses....
[...]
...Likelihood ratio tests (Goldman, 1993; Huelsenbeck and Crandall, 1997), as implemented in MODELTEST 3.06 (Posada and Crandall, 1998), were employed to choose models for ML and ME analyses....
[...]

Reference Entry•DOI•

PAUP* [Phylogenetic Analysis Using Parsimony (and Other Methods)]

[...]

Michael P. Cummings

15 Oct 2004-Dictionary of Bioinformatics and Computational Biology

18,553 citations

"Repeatability of clades as a criter..." refers methods in this paper

...Phylogenetic trees were reconstructed by unweighted maximum parsimony (MP) and model based methods: minimum evolution (ME; Rzhetsky and Nei, 1992) and Maximum Likelihood (ML; Felsenstein, 1981), as im- plemented in PAUP* version 4.0b8 (Swofford, 2001)....
[...]
...…are generally more consistent than trees constructed by equal weighted MP method, which are more sensitive to long branch attraction (Huelsenbeck and Hillis, 1993; Sullivan and Swofford, 2001); and (2) ML trees obtained here rely only on less rigorous heuristic searches (using NNI branch swapping)....
[...]