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Items: 1 to 20 of 104

1.

Studying Evolutionary Dynamics of Gene Families Encoding SUMO-Activating Enzymes with SeaView and ProtTest.

Carretero-Paulet L, Albert VA.

Methods Mol Biol. 2016;1450:273-84. doi: 10.1007/978-1-4939-3759-2_22.

PMID:
27424762
2.

SeaView version 4: A multiplatform graphical user interface for sequence alignment and phylogenetic tree building.

Gouy M, Guindon S, Gascuel O.

Mol Biol Evol. 2010 Feb;27(2):221-4. doi: 10.1093/molbev/msp259. Epub 2009 Oct 23.

PMID:
19854763
3.

MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods.

Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S.

Mol Biol Evol. 2011 Oct;28(10):2731-9. doi: 10.1093/molbev/msr121. Epub 2011 May 4.

4.

Bayesian coestimation of phylogeny and sequence alignment.

Lunter G, Miklós I, Drummond A, Jensen JL, Hein J.

BMC Bioinformatics. 2005 Apr 1;6:83.

5.

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. doi: 10.1186/1471-2148-8-95.

6.

SEAVIEW and PHYLO_WIN: two graphic tools for sequence alignment and molecular phylogeny.

Galtier N, Gouy M, Gautier C.

Comput Appl Biosci. 1996 Dec;12(6):543-8.

PMID:
9021275
7.

Phylogenetic and Evolutionary Analysis of Plant ARGONAUTES.

Singh RK, Pandey SP.

Methods Mol Biol. 2017;1640:267-294. doi: 10.1007/978-1-4939-7165-7_20.

PMID:
28608350
8.

On the quality of tree-based protein classification.

Lazareva-Ulitsky B, Diemer K, Thomas PD.

Bioinformatics. 2005 May 1;21(9):1876-90. Epub 2005 Jan 12.

PMID:
15647305
10.

Pandit: a database of protein and associated nucleotide domains with inferred trees.

Whelan S, de Bakker PI, Goldman N.

Bioinformatics. 2003 Aug 12;19(12):1556-63.

PMID:
12912837
11.

ProtTest: selection of best-fit models of protein evolution.

Abascal F, Zardoya R, Posada D.

Bioinformatics. 2005 May 1;21(9):2104-5. Epub 2005 Jan 12.

PMID:
15647292
12.

CLUSS: clustering of protein sequences based on a new similarity measure.

Kelil A, Wang S, Brzezinski R, Fleury A.

BMC Bioinformatics. 2007 Aug 4;8:286.

13.

DISTREE: a tool for estimating genetic distances between aligned DNA sequences.

Schäfer J, Schöniger M.

Comput Appl Biosci. 1997 Aug;13(4):445-51.

PMID:
9283760
14.

Comparative study of the effectiveness and limitations of current methods for detecting sequence coevolution.

Mao W, Kaya C, Dutta A, Horovitz A, Bahar I.

Bioinformatics. 2015 Jun 15;31(12):1929-37. doi: 10.1093/bioinformatics/btv103. Epub 2015 Feb 19.

15.

JEvTrace: refinement and variations of the evolutionary trace in JAVA.

Joachimiak MP, Cohen FE.

Genome Biol. 2002;3(12):RESEARCH0077. Epub 2002 Nov 26.

16.

Phylogeny-aware alignment with PRANK.

Löytynoja A.

Methods Mol Biol. 2014;1079:155-70. doi: 10.1007/978-1-62703-646-7_10.

PMID:
24170401
17.

LMAP: Lightweight Multigene Analyses in PAML.

Maldonado E, Almeida D, Escalona T, Khan I, Vasconcelos V, Antunes A.

BMC Bioinformatics. 2016 Sep 6;17(1):354. doi: 10.1186/s12859-016-1204-5.

18.

jModelTest: phylogenetic model averaging.

Posada D.

Mol Biol Evol. 2008 Jul;25(7):1253-6. doi: 10.1093/molbev/msn083. Epub 2008 Apr 8.

PMID:
18397919
19.

PAMLX: a graphical user interface for PAML.

Xu B, Yang Z.

Mol Biol Evol. 2013 Dec;30(12):2723-4. doi: 10.1093/molbev/mst179. Epub 2013 Oct 7.

PMID:
24105918
20.

BranchClust: a phylogenetic algorithm for selecting gene families.

Poptsova MS, Gogarten JP.

BMC Bioinformatics. 2007 Apr 10;8:120.

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