00518nas a2200145 4500008004100000245007500041210006900116300001200185490000700197653001400204653001800218653000800236100001800244856011000262 1999 eng d00aFixed character states and the optimization of molecular sequence data0 aFixed character states and the optimization of molecular sequenc a379-3850 v1510aalignment10aphylogenetics10apoy1 aWheeler, Ward uhttps://pterioidea.myspecies.info/content/fixed-character-states-and-optimization-molecular-sequence-data00639nas a2200181 4500008004100000245009500041210006900136300001200205490000700217653001400224653001500238653001800253653000800271653001600279653001200295100002200307856012800329 1995 eng d00aSequence alignment, parameter sensitivity, and the phylogenetic analysis of molecular data0 aSequence alignment parameter sensitivity and the phylogenetic an a321-3310 v4410aalignment10acongruence10aphylogenetics10apoy10asensitivity10asupport1 aWheeler, Ward, C. uhttps://pterioidea.myspecies.info/content/sequence-alignment-parameter-sensitivity-and-phylogenetic-analysis-molecular-data00549nas a2200145 4500008004100000245008500041210006900126300000800195653001400203653002400217653001700241653000800258100002200266856011500288 1996 eng d00aOptimization alignment: the end of multiple sequence alignment in phylogenetics?0 aOptimization alignment the end of multiple sequence alignment in a1-910aalignment10adirect optimization10aoptimization10apoy1 aWheeler, Ward, C. uhttps://pterioidea.myspecies.info/content/optimization-alignment-end-multiple-sequence-alignment-phylogenetics00657nas a2200169 4500008004100000245011100041210006900152300001200221490000700233653001400240653002400254653002200278653001800300653000800318100002200326856013900348 2003 eng d00aImplied alignment: a synapomorphy-based multiple-sequence alignment method and its use in cladogram search0 aImplied alignment a synapomorphybased multiplesequence alignment a261-2680 v1910aalignment10adirect optimization10aimplied alignment10aphylogenetics10apoy1 aWheeler, Ward, C. uhttps://pterioidea.myspecies.info/content/implied-alignment-synapomorphy-based-multiple-sequence-alignment-method-and-its-use-cladogra00502nas a2200145 4500008004100000245006200041210006200103300001400165490001500179653001400194653001200208100001500220700001700235856010400252 1991 eng d00aHistone and histone gene compilation and alignment update0 aHistone and histone gene compilation and alignment update a2173-21880 v19, suppl.10aalignment10ahistone1 aWells, Dan1 aBrown, Doris uhttps://pterioidea.myspecies.info/content/histone-and-histone-gene-compilation-and-alignment-update00724nas a2200193 4500008004100000245012000041210006900161300001400230490000700244653001400251653001200265653001800277100002100295700001900316700001700335700001900352700002000371856013900391 1997 eng d00aThe ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools0 aClustalX windows interface flexible strategies for multiple sequ a4876-48820 v2410aalignment10aclustal10aphylogenetics1 aThompson, J., D.1 aGibson, T., J.1 aPlewniak, F.1 aJeanmougin, F.1 aHiggins, D., G. uhttps://pterioidea.myspecies.info/content/clustalx-windows-interface-flexible-strategies-multiple-sequence-alignment-aided-quality-ana00561nas a2200157 4500008004100000245007500041210006900116300001400185490000600199653001400205653002500219653001800244100002000262700001600282856010500298 1997 eng d00aThe deferred path heuristic for the generalized tree alignment problem0 adeferred path heuristic for the generalized tree alignment probl a415–4310 v410aalignment10amolecular characters10aphylogenetics1 aSchwikowski, B.1 aVingron, M. uhttps://pterioidea.myspecies.info/content/deferred-path-heuristic-generalized-tree-alignment-problem02479nas a2200265 4500008004100000245010000041210006900141260000800210300001200218490000700230520173500237653001401972653001501986653002402001653001502025653001002040653001702050653001802067653000802085653001602093100002102109700002002130700002202150856004102172 2002 eng d00aSimultaneous analysis of the basal lineages of Hymenoptera (Insecta) using sensitivity analysis0 aSimultaneous analysis of the basal lineages of Hymenoptera Insec cOCT a455-4840 v183 aThe first simultaneous analysis of molecular and morphological data of basal hymenopterans that includes exemplars from all families is presented. DNA sequences (of approximately 2000-2700 by for each taxon) from the nuclear genes 18S and 285 and the mitochondrial genes 16S and CO1 have been sequenced for 39 taxa (four outgroup taxa, 29 symphytans, and six apocritans). These DNA sequences and 236 morphological characters from Vihelmsen [Zool. J. Linnean Soc. 131 (2001) 393] were analyzed separately as well as simultaneously. All analyses were performed on unaligned sequences, using the optimization alignment (= direct optimization) method. Sensitivity analysis sensu Wheeler [Syst. Biol. 44 (1995) 321] was applied by analyzing the data under nine different combinations of analysis parameter values. The superfamily level relationships of basal hymenopterans as proposed by Vilhelmsen [Zool. J. Linnean Soc. 131 (2001) 393] and Ronquist et al. [Zool. Scr. 28 (1999) 13] are mostly confirmed, except that Pamphilioidea is the sister group to Tenthredinoidea s.l. and that Anaxyelidae (i.e., Syntexis libocedrii) and Siricidae are supported as a monophyletic group, partly reestablishing the traditional concept of Siricoidea. The resulting hypothesis that best represents the combined evidence from morphology and DNA. sequences is (Xyeloidea (Tenthredinoidea s.l. Pamphilioidea) (Cephoidea (Siricoidea (Xiphydrioidea (Orussidae Apocrita))))), with Siricoidea = Anaxyelidae + Siricidae. The phylogenetic system within Tenthredinoidea s.l., derived from the combined evidence, is (Blasticotomidae (Tenthredinidae including Diprionidae (Cimbicidae (Argidae Pergidae)))). (C) 2002 Elsevier Science (USA). All rights reserved.10aalignment10acongruence10adirect optimization10amorphology10amtDNA10aoptimization10aphylogenetics10apoy10asensitivity1 aSchulmeister, S.1 aWheeler, W., C.1 aCarpenter, J., M. u://00017906150000100505nas a2200157 4500008004100000245005700041210005700098300001000155490000700165653001400172653001300186653001400199653000800213100002700221856009900248 2006 eng d00aHomology assessment and molecular sequence alignment0 aHomology assessment and molecular sequence alignment a18-330 v3910aalignment10ahomology10amolecules10apoy1 aPhillips, Aloysius, J. uhttps://pterioidea.myspecies.info/content/homology-assessment-and-molecular-sequence-alignment00559nas a2200169 4500008004100000245005800041210005800099300001400157490000700171653001400178653001300192653001400205653003200219653001800251100002400269856009600293 2006 eng d00aMultiple sequence alignment for phylogenetic purposes0 aMultiple sequence alignment for phylogenetic purposes a479–5390 v1910aalignment10ahomology10amolecules10amultiple sequence alignment10aphylogenetics1 aMorrison, David, A. uhttps://pterioidea.myspecies.info/content/multiple-sequence-alignment-phylogenetic-purposes00629nas a2200169 4500008004100000245009800041210006900139300001400208490000800222653001400230653000800244653001300252653001800265100002100283700001800304856013700322 2008 eng d00aPhylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis0 aPhylogenyaware gap placement prevents errors in sequence alignme a1632-16350 v32010aalignment10agap10ahomology10aphylogenetics1 aLöytynoja, Ari1 aGoldman, Nick uhttps://pterioidea.myspecies.info/content/phylogeny-aware-gap-placement-prevents-errors-sequence-alignment-and-evolutionary-analysis00814nas a2200289 4500008004100000245004000041210003900081300001400120490000700134653001400141653003200155653001800187100001900205700002100224700001800245700001500263700002300278700001800301700001700319700002000336700001300356700001400369700002100383700001900404700002000423856008100443 2007 eng d00aClustal W and Clustal X version 2.00 aClustal W and Clustal X version 20 a2947-29480 v2310aalignment10amultiple sequence alignment10aphylogenetics1 aLarkin, M., A.1 aBlackshields, G.1 aBrown, N., P.1 aChenna, R.1 aMcGettigan, P., A.1 aMcWilliam, H.1 aValentin, F.1 aWallace, I., M.1 aWilm, A.1 aLopez, R.1 aThompson, J., D.1 aGibson, T., J.1 aHiggins, D., G. uhttps://pterioidea.myspecies.info/content/clustal-w-and-clustal-x-version-2000575nas a2200157 4500008004100000245007800041210006900119300001400188653001400202653002500216653001800241100001400259700001900273700001300292856011200305 1994 eng d00aAligning sequences via an evolutionary tree: complexity and approximation0 aAligning sequences via an evolutionary tree complexity and appro a760–76910aalignment10amolecular characters10aphylogenetics1 aJiang, T.1 aLawler, E., L.1 aWang, A. uhttps://pterioidea.myspecies.info/content/aligning-sequences-evolutionary-tree-complexity-and-approximation00634nas a2200145 4500008004100000245014900041210006900190300001400259490000600273653001400279653002500293653001800318100001300336856013900349 1989 eng d00aA new method that simultaneously aligns and reconstructs ancestral sequences for any number of homologous sequences, when the phylogeny is given0 anew method that simultaneously aligns and reconstructs ancestral a649–6680 v610aalignment10amolecular characters10aphylogenetics1 aHein, J. uhttps://pterioidea.myspecies.info/content/new-method-simultaneously-aligns-and-reconstructs-ancestral-sequences-any-number-homologous-00558nas a2200145 4500008004100000245009500041210006900136300001400205490000600219653001400225653002500239653001800264100001300282856011700295 1989 eng d00aA tree reconstruction method that is economical in the number of pairwise comparisons used0 atree reconstruction method that is economical in the number of p a669–6840 v610aalignment10amolecular characters10aphylogenetics1 aHein, J. uhttps://pterioidea.myspecies.info/content/tree-reconstruction-method-economical-number-pairwise-comparisons-used00660nas a2200193 4500008004100000245009500041210006900136300001000205490000700215653000800222653000800230653001400238653000900252653002400261100002200285700001800307700002000325856012100345 1994 eng d00aLessons from an evolving rRNA: 16S and 23S r RNA structures from a comparative perspective0 aLessons from an evolving rRNA 16S and 23S r RNA structures from a10-260 v5810a16S10a23S10aalignment10arDNA10asecondary structure1 aGutell, Robin, R.1 aLarsen, Niels1 aWoese, Carl, R. uhttps://pterioidea.myspecies.info/content/lessons-evolving-rrna-16s-and-23s-r-rna-structures-comparative-perspective00512nas a2200157 4500008004100000245006000041210005700101300001400158490000800172653001400180653000800194653002500202653001800227100001400245856009500259 1982 eng d00aAn improved algorithm for matching biological sequences0 aimproved algorithm for matching biological sequences a705–7080 v16210aalignment10agap10amolecular characters10aphylogenetics1 aGotoh, O. uhttps://pterioidea.myspecies.info/content/improved-algorithm-matching-biological-sequences01867nas a2200217 4500008004100000245021300041210006900254260000800323300001200331490000700343520111800350653001401468653001801482653000801500653001601508100002201524700002601546700001701572700001901589856004101608 2001 eng d00aPhylogenetics of the lizard genus Tropidurus (Squamata : Tropiduridae : Tropidurinae): Direct optimization, descriptive efficiency, and sensitivity analysis of congruence between molecular data and morphology0 aPhylogenetics of the lizard genus Tropidurus Squamata Tropidurid cDEC a352-3710 v213 aBy use of the technique of direct optimization the phylogenetics of the cis-Andean lizard genus Tropidurus were examined on the basis of both molecular (ca. 1.04 kb of sequences from 12S rDNA, valine tDNA, and 16S rDNA) and morphological (93 characters) data. Although equal weighting of all parsimony cost functions logically must maximize descriptive efficiency and explanatory power of all evidence, a sensitivity analysis demonstrated that equal weighting of indels, transitions, transversions, and morphological change provided the most congruent solution between the molecular and the morphological data partitions. The position of Uranoscodon is resolved as the sister taxon of the remaining members of the Tropidurinae. Plica, Uracentron, and Strobilurus, previously considered synonyms of Tropidurus, are resurrected; the group of these three genera form the sister taxon of the former Tropidurus nanuzae group (herein named Eurolophosaurus) plus Tropidurus sensu stricto (composed of the T. bogerti, T. semitaeniatus, T. spinulosus, and T. torquatus groups, herein diagnosed). (C) 2001 Elsevier Science.10aalignment10aphylogenetics10apoy10asensitivity1 aFrost, Darrel, R.1 aRodrigues, Miguel, T.1 aGrant, Taran1 aTitus, Tom, A. u://00017325130000300487nas a2200169 4500008004100000245003800041210003800079300001200117490000800129653001400137100002100151700001300172700001500185700001800200700001900218856008000237 1990 eng d00aBasic local alignment search tool0 aBasic local alignment search tool a403-4100 v21510aalignment1 aAltschul, S., F.1 aGish, W.1 aMiller, W.1 aMyers, E., W.1 aLipman, D., J. uhttps://pterioidea.myspecies.info/content/basic-local-alignment-search-tool00669nas a2200193 4500008004100000245008500041210006900126300001400195490000700209653001400216100002100230700001900251700002200270700001400292700001400306700001500320700001900335856012100354 1997 eng d00aGapped BLAST and PSI-BLAST: a new generation of protein database search programs0 aGapped BLAST and PSIBLAST a new generation of protein database s a3389-34020 v2510aalignment1 aAltschul, S., F.1 aMadden, T., L.1 aSchäffer, A., A.1 aZhang, J.1 aZhang, Z.1 aMiller, W.1 aLipman, D., J. uhttps://pterioidea.myspecies.info/content/gapped-blast-and-psi-blast-new-generation-protein-database-search-programs