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Results: 1 to 20 of 117

1.

Noisy: identification of problematic columns in multiple sequence alignments.

Dress AW, Flamm C, Fritzsch G, Grünewald S, Kruspe M, Prohaska SJ, Stadler PF.

Algorithms Mol Biol. 2008 Jun 24;3:7.PMID: 18577231 [PubMed]Related articlesFree article

2.

Using ESTs for phylogenomics: can one accurately infer a phylogenetic tree from a gappy alignment?

Hartmann S, Vision TJ.

BMC Evol Biol. 2008 Mar 26;8:95.PMID: 18366758 [PubMed - indexed for MEDLINE]Related articlesFree article

3.

NcDNAlign: plausible multiple alignments of non-protein-coding genomic sequences.

Rose D, Hertel J, Reiche K, Stadler PF, Hackermüller J.

Genomics. 2008 Jul;92(1):65-74. Epub 2008 Jun 3.PMID: 18511233 [PubMed - indexed for MEDLINE]Related articles

4.

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 articles

5.

Phylogenetic supermatrix analysis of GenBank sequences from 2228 papilionoid legumes.

McMahon MM, Sanderson MJ.

Syst Biol. 2006 Oct;55(5):818-36.PMID: 17060202 [PubMed - indexed for MEDLINE]Related articles

6.

Construction of evolutionary distance trees with TREECON for Windows: accounting for variation in nucleotide substitution rate among sites.

Van de Peer Y, De Wachter R.

Comput Appl Biosci. 1997 Jun;13(3):227-30.PMID: 9183524 [PubMed - indexed for MEDLINE]Related articles

7.

Pattern-based phylogenetic distance estimation and tree reconstruction.

Höhl M, Rigoutsos I, Ragan MA.

Evol Bioinform Online. 2007 Feb 25;2:359-75.PMID: 19455227 [PubMed - in process]Related articlesFree article

8.

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]Related articlesFree article

9.

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]Related articlesFree article

10.

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]Related articlesFree article

11.

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]Related articlesFree article

12.

Web-links as a means to document annotated sequence and 3D-structure alignments in systems biology.

Gille C, Hoppe A, Holzhütter HG.

Genome Inform. 2008;20:277-84.PMID: 19425142 [PubMed - indexed for MEDLINE]Related articlesFree article

13.

StatAlign: an extendable software package for joint Bayesian estimation of alignments and evolutionary trees.

Novák A, Miklós I, Lyngsø R, Hein J.

Bioinformatics. 2008 Oct 15;24(20):2403-4. Epub 2008 Aug 27.PMID: 18753153 [PubMed - indexed for MEDLINE]Related articlesFree article

14.

Methods for multiple alignment and consensus structure prediction of RNAs implemented in MARNA.

Siebert S, Backofen R.

Methods Mol Biol. 2007;395:489-502.PMID: 17993694 [PubMed - indexed for MEDLINE]Related articles

15.

Removal of noisy characters from chloroplast genome-scale data suggests revision of phylogenetic placements of Amborella and Ceratophyllum.

Goremykin VV, Viola R, Hellwig FH.

J Mol Evol. 2009 Mar;68(3):197-204. Epub 2009 Feb 27.PMID: 19247564 [PubMed - indexed for MEDLINE]Related articles

16.

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]Related articlesFree article

17.

Assessing the performance of single-copy genes for recovering robust phylogenies.

Aguileta G, Marthey S, Chiapello H, Lebrun MH, Rodolphe F, Fournier E, Gendrault-Jacquemard A, Giraud T.

Syst Biol. 2008 Aug;57(4):613-27.PMID: 18709599 [PubMed - in process]Related articles

18.

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]Related articles

19.

SynBlast: assisting the analysis of conserved synteny information.

Lehmann J, Stadler PF, Prohaska SJ.

BMC Bioinformatics. 2008 Aug 24;9:351.PMID: 18721485 [PubMed - indexed for MEDLINE]Related articlesFree article

20.

LineageSpecificSeqgen: generating sequence data with lineage-specific variation in the proportion of variable sites.

Shavit Grievink L, Penny D, Hendy MD, Holland BR.

BMC Evol Biol. 2008 Nov 21;8:317. Erratum in: BMC Evol Biol. 2009;9:200. doi:10.1186/1471-2148-9-200. PMID: 19021917 [PubMed - indexed for MEDLINE]Related articlesFree article

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