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Ultra-large alignments using phylogeny-aware profiles.

Nguyen NP, Mirarab S, Kumar K, Warnow T.

Genome Biol. 2015 Jun 16;16(1):124. [Epub ahead of print]


Current methods for automated filtering of multiple sequence alignments frequently worsen single-gene phylogenetic inference.

Tan G, Muffato M, Ledergerber C, Herrero J, Goldman N, Gil M, Dessimoz C.

Syst Biol. 2015 Jun 1. pii: syv033. [Epub ahead of print]


UrQt: an efficient software for the Unsupervised Quality trimming of NGS data.

Modolo L, Lerat E.

BMC Bioinformatics. 2015 Apr 29;16:137. doi: 10.1186/s12859-015-0546-8.


Automatic selection of partitioning schemes for phylogenetic analyses using iterative k-means clustering of site rates.

Frandsen PB, Calcott B, Mayer C, Lanfear R.

BMC Evol Biol. 2015 Feb 10;15:13. doi: 10.1186/s12862-015-0283-7.


IVisTMSA: Interactive Visual Tools for Multiple Sequence Alignments.

Pervez MT, Babar ME, Nadeem A, Aslam N, Naveed N, Ahmad S, Muhammad S, Qadri S, Shahid M, Hussain T, Javed M.

Evol Bioinform Online. 2015 Mar 12;11:35-42. doi: 10.4137/EBO.S18980. eCollection 2015. Review.


A new method to cluster DNA sequences using Fourier power spectrum.

Hoang T, Yin C, Zheng H, Yu C, Lucy He R, Yau SS.

J Theor Biol. 2015 May 7;372:135-45. doi: 10.1016/j.jtbi.2015.02.026. Epub 2015 Mar 5.


This special issue includes a selection of papers presented at the 2nd IEEE International Conference. Introduction.

Mandoiu I, Pop M, Rajasekaran S, Spouge JL.

Int J Bioinform Res Appl. 2014;10(4-5):341-4. No abstract available.


Rock, paper, scissors: harnessing complementarity in ortholog detection methods improves comparative genomic inference.

Maher MC, Hernandez RD.

G3 (Bethesda). 2015 Feb 23;5(4):629-38. doi: 10.1534/g3.115.017095.


MatrixConverter: Facilitating construction of phenomic character matrices.

Liu J, Endara L, Burleigh JG.

Appl Plant Sci. 2015 Feb 9;3(2). pii: apps.1400088. doi: 10.3732/apps.1400088. eCollection 2015 Feb.


Simple chained guide trees give poorer multiple sequence alignments than inferred trees in simulation and phylogenetic benchmarks.

Tan G, Gil M, Löytynoja AP, Goldman N, Dessimoz C.

Proc Natl Acad Sci U S A. 2015 Jan 13;112(2):E99-100. doi: 10.1073/pnas.1417526112. Epub 2015 Jan 6. No abstract available.


PASTA: Ultra-Large Multiple Sequence Alignment for Nucleotide and Amino-Acid Sequences.

Mirarab S, Nguyen N, Guo S, Wang LS, Kim J, Warnow T.

J Comput Biol. 2015 May;22(5):377-86. doi: 10.1089/cmb.2014.0156. Epub 2014 Dec 30.


SWAMP: Sliding Window Alignment Masker for PAML.

Harrison PW, Jordan GE, Montgomery SH.

Evol Bioinform Online. 2014 Dec 1;10:197-204. doi: 10.4137/EBO.S18193. eCollection 2014.


FASconCAT-G: extensive functions for multiple sequence alignment preparations concerning phylogenetic studies.

Kück P, Longo GC.

Front Zool. 2014 Nov 18;11(1):81. doi: 10.1186/s12983-014-0081-x. eCollection 2014.


DivA: detection of non-homologous and very divergent regions in protein sequence alignments.

Zepeda Mendoza ML, Nygaard S, da Fonseca RR.

BMC Res Notes. 2014 Nov 18;7:806. doi: 10.1186/1756-0500-7-806.


Sequence exploration reveals information bias among molecular markers used in phylogenetic reconstruction for Colletotrichum species.

Rampersad SN, Hosein FN, Carrington CV.

Springerplus. 2014 Oct 17;3:614. doi: 10.1186/2193-1801-3-614. eCollection 2014.


Alignathon: a competitive assessment of whole-genome alignment methods.

Earl D, Nguyen N, Hickey G, Harris RS, Fitzgerald S, Beal K, Seledtsov I, Molodtsov V, Raney BJ, Clawson H, Kim J, Kemena C, Chang JM, Erb I, Poliakov A, Hou M, Herrero J, Kent WJ, Solovyev V, Darling AE, Ma J, Notredame C, Brudno M, Dubchak I, Haussler D, Paten B.

Genome Res. 2014 Dec;24(12):2077-89. doi: 10.1101/gr.174920.114. Epub 2014 Oct 1.


Inferring phylogenies of evolving sequences without multiple sequence alignment.

Chan CX, Bernard G, Poirion O, Hogan JM, Ragan MA.

Sci Rep. 2014 Sep 30;4:6504. doi: 10.1038/srep06504.


An improved alignment-free model for DNA sequence similarity metric.

Bao J, Yuan R, Bao Z.

BMC Bioinformatics. 2014 Sep 28;15:321. doi: 10.1186/1471-2105-15-321.


SDT: a virus classification tool based on pairwise sequence alignment and identity calculation.

Muhire BM, Varsani A, Martin DP.

PLoS One. 2014 Sep 26;9(9):e108277. doi: 10.1371/journal.pone.0108277. eCollection 2014.

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