{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,24]],"date-time":"2026-06-24T21:42:47Z","timestamp":1782337367014,"version":"3.54.5"},"reference-count":55,"publisher":"Oxford University Press (OUP)","issue":"4","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2007,8,1]]},"DOI":"10.1080\/10635150701472164","type":"journal-article","created":{"date-parts":[[2007,7,26]],"date-time":"2007-07-26T04:24:40Z","timestamp":1185423880000},"page":"564-577","source":"Crossref","is-referenced-by-count":5006,"title":["Improvement of Phylogenies after Removing Divergent and Ambiguously Aligned Blocks from Protein Sequence Alignments"],"prefix":"10.1093","volume":"56","author":[{"given":"Gerard","family":"Talavera","sequence":"first","affiliation":[{"name":"Department of Physiology and Molecular Biodiversity, Institute of Molecular Biology of Barcelona CSIC, Jordi Girona 18, Barcelona, 08034, Spain E-mail: jcvagr@ibmb.csic.es (J.C.)"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jose","family":"Castresana","sequence":"additional","affiliation":[{"name":"Department of Physiology and Molecular Biodiversity, Institute of Molecular Biology of Barcelona CSIC, Jordi Girona 18, Barcelona, 08034, Spain E-mail: jcvagr@ibmb.csic.es (J.C.)"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2007,8]]},"reference":[{"key":"key\n\t\t\t\t20180228064204_b1","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1016\/j.ode.2003.11.003","article-title":"The information content of an ambiguously alignable region, a case study of the trnL intron from the Rhamnaceae","volume":"4","author":"Aagesen","year":"2004","journal-title":"Organ. Divers. Evol."},{"key":"key\n\t\t\t\t20180228064204_b2","first-page":"321","article-title":"Analysis and comparison of benchmarks for multiple sequence alignment","volume":"6","author":"Blackshields","year":"2006","journal-title":"In Silico Biol."},{"key":"key\n\t\t\t\t20180228064204_b3","doi-asserted-by":"crossref","first-page":"540","DOI":"10.1093\/oxfordjournals.molbev.a026334","article-title":"Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis","volume":"17","author":"Castresana","year":"2000","journal-title":"Mol. Biol. Evol."},{"key":"key\n\t\t\t\t20180228064204_b4","doi-asserted-by":"crossref","first-page":"3703","DOI":"10.1073\/pnas.95.7.3703","article-title":"Codon reassignment and amino acid composition in hemichordate mitochondria","volume":"95","author":"Castresana","year":"1998","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"key\n\t\t\t\t20180228064204_b5","doi-asserted-by":"crossref","first-page":"1115","DOI":"10.1093\/genetics\/150.3.1115","article-title":"The mitochondrial genome of the hemichordate Balanoglossus carnosus and the evolution of deuterostome mitochondria","volume":"150","author":"Castresana","year":"1998","journal-title":"Genetics"},{"key":"key\n\t\t\t\t20180228064204_b6","first-page":"345","article-title":"A model of evolutionary change in proteins","volume-title":"Atlas of protein sequence structure","author":"Dayhoff","year":"1978"},{"key":"key\n\t\t\t\t20180228064204_b7","doi-asserted-by":"crossref","first-page":"361","DOI":"10.1038\/nrg1603","article-title":"Phylogenomics and the reconstruction of the tree of life","volume":"6","author":"Delsuc","year":"2005","journal-title":"Nat. Rev. Genet."},{"key":"key\n\t\t\t\t20180228064204_b8","doi-asserted-by":"crossref","first-page":"330","DOI":"10.1101\/gr.2821705","article-title":"ProbCons: Probabilistic consistency-based multiple sequence alignment","volume":"15","author":"Do","year":"2005","journal-title":"Genome Res."},{"key":"key\n\t\t\t\t20180228064204_b9","doi-asserted-by":"crossref","first-page":"662","DOI":"10.1093\/bioinformatics\/17.7.662","article-title":"PAL: An object-oriented programming library for molecular evolution and phylogenetics","volume":"17","author":"Drummond","year":"2001","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20180228064204_b10","doi-asserted-by":"crossref","first-page":"1792","DOI":"10.1093\/nar\/gkh340","article-title":"MUSCLE: Multiple sequence alignment with high accuracy and high throughput","volume":"32","author":"Edgar","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180228064204_b11","first-page":"164","article-title":"PHYLIP\u2014Phylogeny inference package (version 3.4)","volume":"5","author":"Felsenstein","year":"1989","journal-title":"Cladistics"},{"key":"key\n\t\t\t\t20180228064204_b12","volume-title":"Inferring phylogenies","author":"Felsenstein","year":"2004"},{"key":"key\n\t\t\t\t20180228064204_b13","doi-asserted-by":"crossref","first-page":"351","DOI":"10.1007\/BF02603120","article-title":"Progressive sequence alignment as a prerequisite to correct phylogenetic trees","volume":"25","author":"Feng","year":"1987","journal-title":"J. Mol. Evol."},{"key":"key\n\t\t\t\t20180228064204_b14","doi-asserted-by":"crossref","first-page":"548","DOI":"10.1080\/10635150590950371","article-title":"Simultaneous statistical multiple alignment and phylogeny reconstruction","volume":"54","author":"Fleissner","year":"2005","journal-title":"Syst. Biol."},{"key":"key\n\t\t\t\t20180228064204_b15","doi-asserted-by":"crossref","first-page":"152","DOI":"10.1006\/mpev.1993.1015","article-title":"Alignment-ambiguous nucleotide sites and the exclusion of systematic data","volume":"2","author":"Gatesy","year":"1993","journal-title":"Mol. Phylogenet. Evol."},{"key":"key\n\t\t\t\t20180228064204_b16","doi-asserted-by":"crossref","first-page":"191","DOI":"10.1007\/s00239-001-0001-5","article-title":"Stretch coding and block coding: Two new strategies to represent questionably aligned DNA sequences","volume":"54","author":"Geiger","year":"2002","journal-title":"J. Mol. Evol."},{"key":"key\n\t\t\t\t20180228064204_b17","doi-asserted-by":"crossref","first-page":"128","DOI":"10.1002\/(SICI)1097-010X(19990815)285:2<128::AID-JEZ5>3.0.CO;2-C","article-title":"Phylogenetic inference from conserved sites alignments","volume":"285","author":"Grundy","year":"1999","journal-title":"J. Exp. Zool."},{"key":"key\n\t\t\t\t20180228064204_b18","doi-asserted-by":"crossref","first-page":"696","DOI":"10.1080\/10635150390235520","article-title":"A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood","volume":"52","author":"Guindon","year":"2003","journal-title":"Syst. Biol."},{"key":"key\n\t\t\t\t20180228064204_b19","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1128\/MMBR.58.1.10-26.1994","article-title":"Lessons from an evolving rRNA: 16S and 23S rRNA structures from a comparative perspective","volume":"58","author":"Gutell","year":"1994","journal-title":"Microbiol. Rev."},{"key":"key\n\t\t\t\t20180228064204_b20","doi-asserted-by":"crossref","first-page":"97","DOI":"10.1006\/geno.1994.1018","article-title":"Protein family classification based on searching a database of blocks","volume":"19","author":"Henikoff","year":"1994","journal-title":"Genomics"},{"key":"key\n\t\t\t\t20180228064204_b21","first-page":"197","article-title":"CONRAD: A method for identification of variable and conserved regions within proteins by scale-space filtering","volume":"12","author":"Herrmann","year":"1996","journal-title":"Comput. Appl. Biosci."},{"key":"key\n\t\t\t\t20180228064204_b22","doi-asserted-by":"crossref","first-page":"10411","DOI":"10.1073\/pnas.0504801102","article-title":"Mind the gaps: Progress in progressive alignment","volume":"102","author":"Higgins","year":"2005","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"key\n\t\t\t\t20180228064204_b23","doi-asserted-by":"crossref","first-page":"225","DOI":"10.1016\/j.tig.2006.02.003","article-title":"Phylogenomics: The beginning of incongruence?","volume":"22","author":"Jeffroy","year":"2006","journal-title":"Trends Genet."},{"key":"key\n\t\t\t\t20180228064204_b24","first-page":"275","article-title":"The rapid generation of mutation data matrices from protein sequences","volume":"8","author":"Jones","year":"1992","journal-title":"Comput. Appl. Biosci."},{"key":"key\n\t\t\t\t20180228064204_b25","doi-asserted-by":"crossref","first-page":"511","DOI":"10.1093\/nar\/gki198","article-title":"MAFFT version 5: Improvement in accuracy of multiple sequence alignment","volume":"33","author":"Katoh","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180228064204_b26","doi-asserted-by":"crossref","first-page":"3059","DOI":"10.1093\/nar\/gkf436","article-title":"MAFFT: A novel method for rapid multiple sequence alignment based on fast Fourier transform","volume":"30","author":"Katoh","year":"2002","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180228064204_b27","doi-asserted-by":"crossref","first-page":"314","DOI":"10.1006\/mpev.1995.1028","article-title":"Use of rRNA secondary structure in phylogenetic studies to identify homologous positions: an example of alignment and data presentation from the frogs","volume":"4","author":"Kjer","year":"1995","journal-title":"Mol. Phylogenet. Evol."},{"key":"key\n\t\t\t\t20180228064204_b28","first-page":"378","article-title":"The order of sequence alignment can bias the selection of tree topology","volume":"8","author":"Lake","year":"1991","journal-title":"Mol. Biol. Evol."},{"key":"key\n\t\t\t\t20180228064204_b29","doi-asserted-by":"crossref","first-page":"298","DOI":"10.1186\/1471-2105-6-298","article-title":"Kalign\u2014An accurate and fast multiple sequence alignment algorithm","volume":"6","author":"Lassmann","year":"2005","journal-title":"BMC Bioinformatics"},{"key":"key\n\t\t\t\t20180228064204_b30","doi-asserted-by":"crossref","first-page":"681","DOI":"10.1016\/S0169-5347(01)02313-8","article-title":"Unalignable sequences and molecular evolution","volume":"16","author":"Lee","year":"2001","journal-title":"Trends Ecol. Evol."},{"key":"key\n\t\t\t\t20180228064204_b31","doi-asserted-by":"crossref","first-page":"573","DOI":"10.1093\/bioinformatics\/17.6.573","article-title":"SOAP, cleaning multiple alignments from unstable blocks","volume":"17","author":"L\u00f6ytynoja","year":"2001","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20180228064204_b32","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1186\/1471-2105-6-83","article-title":"Bayesian coestimation of phylogeny and sequence alignment","volume":"6","author":"Lunter","year":"2005","journal-title":"BMC Bioinformatics"},{"key":"key\n\t\t\t\t20180228064204_b33","doi-asserted-by":"crossref","first-page":"628","DOI":"10.1080\/106351500750049743","article-title":"Integrating ambiguously aligned regions of DNA sequences in phylogenetic analyses without violating positional homology","volume":"49","author":"Lutzoni","year":"2000","journal-title":"Syst. Biol."},{"key":"key\n\t\t\t\t20180228064204_b34","doi-asserted-by":"crossref","first-page":"428","DOI":"10.1093\/oxfordjournals.molbev.a025779","article-title":"Effects of nucleotide sequence alignment on phylogeny estimation: A case study of 18S rDNAs of apicomplexa","volume":"14","author":"Morrison","year":"1997","journal-title":"Mol. Biol. Evol."},{"key":"key\n\t\t\t\t20180228064204_b35","doi-asserted-by":"crossref","first-page":"443","DOI":"10.1016\/0022-2836(70)90057-4","article-title":"A general method applicable to the search for similarities in the amino acid sequence of two proteins","volume":"48","author":"Needleman","year":"1970","journal-title":"J. Mol. Biol."},{"key":"key\n\t\t\t\t20180228064204_b36","doi-asserted-by":"crossref","first-page":"205","DOI":"10.1006\/jmbi.2000.4042","article-title":"T-Coffee: A novel method for fast and accurate multiple sequence alignment","volume":"302","author":"Notredame","year":"2000","journal-title":"J. Mol. Biol."},{"key":"key\n\t\t\t\t20180228064204_b37","doi-asserted-by":"crossref","first-page":"471","DOI":"10.1186\/1471-2105-7-471","article-title":"The accuracy of several multiple sequence alignment programs for proteins","volume":"7","author":"Nuin","year":"2006","journal-title":"BMC Bioinformatics"},{"key":"key\n\t\t\t\t20180228064204_b38","doi-asserted-by":"crossref","first-page":"314","DOI":"10.1080\/10635150500541730","article-title":"Multiple sequence alignment accuracy and phylogenetic inference","volume":"55","author":"Ogden","year":"2006","journal-title":"Syst. Biol."},{"key":"key\n\t\t\t\t20180228064204_b39","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1016\/1055-7903(92)90023-A","article-title":"A statistical method for detecting regions with different evolutionary dynamics in multialigned sequences","volume":"1","author":"Pesole","year":"1992","journal-title":"Mol. Phylogenet. Evol."},{"key":"key\n\t\t\t\t20180228064204_b40","doi-asserted-by":"crossref","first-page":"616","DOI":"10.1016\/S0959-437X(98)80028-2","article-title":"How good are deep phylogenetic trees? Curr","volume":"8","author":"Philippe","year":"1998","journal-title":"Opin. Genet. Dev."},{"key":"key\n\t\t\t\t20180228064204_b41","doi-asserted-by":"crossref","first-page":"401","DOI":"10.1080\/10635150590947041","article-title":"Joint Bayesian estimation of alignment and phylogeny","volume":"54","author":"Redelings","year":"2005","journal-title":"Syst. Biol."},{"key":"key\n\t\t\t\t20180228064204_b42","doi-asserted-by":"crossref","first-page":"131","DOI":"10.1016\/0025-5564(81)90043-2","article-title":"Comparison of phylogenetic trees","volume":"53","author":"Robinson","year":"1981","journal-title":"Math. Biosci."},{"key":"key\n\t\t\t\t20180228064204_b43","doi-asserted-by":"crossref","first-page":"578","DOI":"10.1093\/sysbio\/43.4.578","article-title":"Inadequate support for an evolutionary link between the Metazoa and the Fungi","volume":"43","author":"Rodrigo","year":"1994","journal-title":"Syst. Biol."},{"key":"key\n\t\t\t\t20180228064204_b44","doi-asserted-by":"crossref","first-page":"972","DOI":"10.1080\/10635150601089001","article-title":"Nematode small subunit phylogeny correlates with alignment parameters","volume":"55","author":"Smythe","year":"2006","journal-title":"Syst. Biol."},{"key":"key\n\t\t\t\t20180228064204_b45","doi-asserted-by":"crossref","first-page":"1611","DOI":"10.1101\/gr.361602","article-title":"The Bioperl toolkit: Perl modules for the life sciences","volume":"12","author":"Stajich","year":"2002","journal-title":"Genome Res."},{"key":"key\n\t\t\t\t20180228064204_b46","doi-asserted-by":"crossref","first-page":"157","DOI":"10.1093\/bioinformatics\/14.2.157","article-title":"Rose: Generating sequence families","volume":"14","author":"Stoye","year":"1998","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20180228064204_b47","doi-asserted-by":"crossref","first-page":"964","DOI":"10.1093\/oxfordjournals.molbev.a025664","article-title":"Quartet puzzling: A quartet maximum-likelihood method for reconstructing tree topologies","volume":"13","author":"Strimmer","year":"1996","journal-title":"Mol. Biol. Evol."},{"key":"key\n\t\t\t\t20180228064204_b48","first-page":"407","article-title":"Phylogenetic inference","volume-title":"Molecular systematics","author":"Swofford","year":"1996"},{"key":"key\n\t\t\t\t20180228064204_b49","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1186\/1471-2105-4-41","article-title":"The COG database: an updated version includes eukaryotes","volume":"4","author":"Tatusov","year":"2003","journal-title":"BMC Bioinformatics"},{"key":"key\n\t\t\t\t20180228064204_b50","doi-asserted-by":"crossref","first-page":"4673","DOI":"10.1093\/nar\/22.22.4673","article-title":"CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice","volume":"22","author":"Thompson","year":"1994","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180228064204_b51","doi-asserted-by":"crossref","first-page":"127","DOI":"10.1002\/prot.20527","article-title":"BAliBASE 3.0: Latest developments of the multiple sequence alignment benchmark","volume":"61","author":"Thompson","year":"2005","journal-title":"Proteins"},{"key":"key\n\t\t\t\t20180228064204_b52","doi-asserted-by":"crossref","first-page":"S3","DOI":"10.1111\/j.1096-0031.2001.tb00100.x","article-title":"Homology and the optimization of DNA sequence data","volume":"17","author":"Wheeler","year":"2001","journal-title":"Cladistics"},{"key":"key\n\t\t\t\t20180228064204_b53","doi-asserted-by":"crossref","first-page":"283","DOI":"10.1080\/10635150390196948","article-title":"18S ribosomal RNA and tetrapod phylogeny","volume":"52","author":"Xia","year":"2003","journal-title":"Syst. Biol."},{"key":"key\n\t\t\t\t20180228064204_b54","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1080\/106351598261067","article-title":"On the best evolutionary rate for phylogenetic analysis","volume":"47","author":"Yang","year":"1998","journal-title":"Syst. Biol."},{"key":"key\n\t\t\t\t20180228064204_b55","doi-asserted-by":"crossref","first-page":"6","DOI":"10.1186\/1471-2105-4-6","article-title":"GapCoder automates the use of indel characters in phylogenetic analysis","volume":"4","author":"Young","year":"2003","journal-title":"BMC Bioinformatics"}],"container-title":["Systematic Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/sysbio\/article-pdf\/56\/4\/564\/24202335\/56-4-564.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,8,20]],"date-time":"2021-08-20T12:15:22Z","timestamp":1629461722000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/sysbio\/article\/56\/4\/564\/1682121"}},"subtitle":[],"editor":[{"given":"Karl","family":"Kjer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]},{"given":"Rod","family":"Page","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]},{"given":"Jack","family":"Sullivan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2007,8,1]]},"references-count":55,"journal-issue":{"issue":"4","published-online":{"date-parts":[[2007,8]]},"published-print":{"date-parts":[[2007,8,1]]}},"URL":"https:\/\/doi.org\/10.1080\/10635150701472164","relation":{},"ISSN":["1076-836X","1063-5157"],"issn-type":[{"value":"1076-836X","type":"electronic"},{"value":"1063-5157","type":"print"}],"subject":[],"published-other":{"date-parts":[[2007,8]]},"published":{"date-parts":[[2007,8,1]]}}}