PubMed

Stability of multiple alignments and phylogenetic trees: an analysis of ABC-transporter proteins family.

Wagner H, Morgenstern B, Dress A.

Algorithms Mol Biol. 2008 Nov 6;3:15.PMID: 18990223 [PubMed]Free PMC ArticleFree textRelated citations

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

Talavera G, Castresana J.

Syst Biol. 2007 Aug;56(4):564-77.PMID: 17654362 [PubMed - indexed for MEDLINE]Related citations

DIALIGN-TX: greedy and progressive approaches for segment-based multiple sequence alignment.

Subramanian AR, Kaufmann M, Morgenstern B.

Algorithms Mol Biol. 2008 May 27;3:6.PMID: 18505568 [PubMed]Free PMC ArticleFree textRelated citations

Simultaneous phylogeny reconstruction and multiple sequence alignment.

Yue F, Shi J, Tang J.

BMC Bioinformatics. 2009 Jan 30;10 Suppl 1:S11.PMID: 19208110 [PubMed - indexed for MEDLINE]Free PMC ArticleFree textRelated citations

Nematode small subunit phylogeny correlates with alignment parameters.

Smythe AB, Sanderson MJ, Nadler SA.

Syst Biol. 2006 Dec;55(6):972-92.PMID: 17345678 [PubMed - indexed for MEDLINE]Related citations

A reality check for alignments and trees.

Martin W, Roettger M, Lockhart PJ.

Trends Genet. 2007 Oct;23(10):478-80. Epub 2007 Sep 7.PMID: 17825944 [PubMed - indexed for MEDLINE]Related citations

OrthoSelect: a protocol for selecting orthologous groups in phylogenomics.

Schreiber F, Pick K, Erpenbeck D, Wörheide G, Morgenstern B.

BMC Bioinformatics. 2009 Jul 16;10:219.PMID: 19607672 [PubMed - indexed for MEDLINE]Free PMC ArticleFree textRelated citations

ProfDistS: (profile-) distance based phylogeny on sequence--structure alignments.

Wolf M, Ruderisch B, Dandekar T, Schultz J, Müller T.

Bioinformatics. 2008 Oct 15;24(20):2401-2. Epub 2008 Aug 21.PMID: 18723521 [PubMed - indexed for MEDLINE]Free ArticleRelated citations

Diversity and evolution of the small multidrug resistance protein family.

Bay DC, Turner RJ.

BMC Evol Biol. 2009 Jun 23;9:140.PMID: 19549332 [PubMed - indexed for MEDLINE]Free PMC ArticleFree textRelated citations

A class frequency mixture model that adjusts for site-specific amino acid frequencies and improves inference of protein phylogeny.

Wang HC, Li K, Susko E, Roger AJ.

BMC Evol Biol. 2008 Dec 16;8:331.PMID: 19087270 [PubMed - indexed for MEDLINE]Free PMC ArticleFree textRelated citations

Multiple sequence alignment with user-defined anchor points.

Morgenstern B, Prohaska SJ, Pöhler D, Stadler PF.

Algorithms Mol Biol. 2006 Apr 19;1(1):6.PMID: 16722533 [PubMed]Free PMC ArticleFree textRelated citations

CLUSTAL V: improved software for multiple sequence alignment.

Higgins DG, Bleasby AJ, Fuchs R.

Comput Appl Biosci. 1992 Apr;8(2):189-91.PMID: 1591615 [PubMed - indexed for MEDLINE]Related citations

CSA: an efficient algorithm to improve circular DNA multiple alignment.

Fernandes F, Pereira L, Freitas AT.

BMC Bioinformatics. 2009 Jul 23;10:230.PMID: 19627599 [PubMed - indexed for MEDLINE]Free PMC ArticleFree textRelated citations

Phylogenetic inference under varying proportions of indel-induced alignment gaps.

Dwivedi B, Gadagkar SR.

BMC Evol Biol. 2009 Aug 23;9:211.PMID: 19698168 [PubMed - indexed for MEDLINE]Free PMC ArticleFree textRelated citations

Phylogenetic support values are not necessarily informative: the case of the Serialia hypothesis (a mollusk phylogeny).

Wägele JW, Letsch H, Klussmann-Kolb A, Mayer C, Misof B, Wägele H.

Front Zool. 2009 Jun 26;6:12.PMID: 19555513 [PubMed - in process]Free PMC ArticleFree textRelated citations

Can comprehensive background knowledge be incorporated into substitution models to improve phylogenetic analyses? A case study on major arthropod relationships.

von Reumont BM, Meusemann K, Szucsich NU, Dell'Ampio E, Gowri-Shankar V, Bartel D, Simon S, Letsch HO, Stocsits RR, Luan YX, Wägele JW, Pass G, Hadrys H, Misof B.

BMC Evol Biol. 2009 May 27;9:119.PMID: 19473484 [PubMed - indexed for MEDLINE]Free PMC ArticleFree textRelated citations

dnaJ is a useful phylogenetic marker for alphaproteobacteria.

Alexandre A, Laranjo M, Young JP, Oliveira S.

Int J Syst Evol Microbiol. 2008 Dec;58(Pt 12):2839-49.PMID: 19060069 [PubMed - indexed for MEDLINE]Related citations

Assessing what is needed to resolve a molecular phylogeny: simulations and empirical data from emydid turtles.

Spinks PQ, Thomson RC, Lovely GA, Shaffer HB.

BMC Evol Biol. 2009 Mar 12;9:56.PMID: 19284630 [PubMed - indexed for MEDLINE]Free PMC ArticleFree textRelated citations

Accurate and efficient reconstruction of deep phylogenies from structured RNAs.

Stocsits RR, Letsch H, Hertel J, Misof B, Stadler PF.

Nucleic Acids Res. 2009 Oct;37(18):6184-93. Epub 2009 Sep 1.PMID: 19723687 [PubMed - indexed for MEDLINE]Free PMC ArticleFree textRelated citations

Rapid and accurate large-scale coestimation of sequence alignments and phylogenetic trees.

Liu K, Raghavan S, Nelesen S, Linder CR, Warnow T.

Science. 2009 Jun 19;324(5934):1561-4.PMID: 19541996 [PubMed - indexed for MEDLINE]Free ArticleRelated citations