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Items: 1 to 20 of 81

1.

Phylogenies scores for exhaustive searches and parsimony scores searches.

Carroll HD, Ridge PG, Clement MJ, Snell QO.

Int J Bioinform Res Appl. 2007;3(4):493-503.

PMID:
18048315
2.

Bayesian coestimation of phylogeny and sequence alignment.

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

BMC Bioinformatics. 2005 Apr 1;6:83.

3.

A generalized affine gap model significantly improves protein sequence alignment accuracy.

Zachariah MA, Crooks GE, Holbrook SR, Brenner SE.

Proteins. 2005 Feb 1;58(2):329-38.

PMID:
15562515
5.

Characterization of multiple sequence alignment errors using complete-likelihood score and position-shift map.

Ezawa K.

BMC Bioinformatics. 2016 Mar 18;17:133. doi: 10.1186/s12859-016-0945-5.

6.

PRec-I-DCM3: a parallel framework for fast and accurate large-scale phylogeny reconstruction.

Dotsenko Y, Coarfa C, Nakhleh L, Mellor-Crummey J, Roshan U.

Int J Bioinform Res Appl. 2006;2(4):407-19.

PMID:
18048181
7.

Direct maximum parsimony phylogeny reconstruction from genotype data.

Sridhar S, Lam F, Blelloch GE, Ravi R, Schwartz R.

BMC Bioinformatics. 2007 Dec 5;8:472.

9.

Evaluating the performance of a successive-approximations approach to parameter optimization in maximum-likelihood phylogeny estimation.

Sullivan J, Abdo Z, Joyce P, Swofford DL.

Mol Biol Evol. 2005 Jun;22(6):1386-92. Epub 2005 Mar 9.

PMID:
15758203
10.
11.

Parsimony accelerated maximum likelihood searches.

Sundberg K, O'Connor T, Carroll H, Clement M, Snell Q.

Int J Comput Biol Drug Des. 2008;1(1):74-87.

PMID:
20055002
12.

Ancestral sequence alignment under optimal conditions.

Hudek AK, Brown DG.

BMC Bioinformatics. 2005 Nov 17;6:273.

13.

Rate-variation need not defeat phylogenetic inference through pairwise sequence comparisons.

Wu J, Susko E.

J Theor Biol. 2010 Apr 21;263(4):587-9. doi: 10.1016/j.jtbi.2009.12.022. Epub 2010 Jan 4. No abstract available.

PMID:
20043922
14.

Statistics of local multiple alignments.

Prakash A, Tompa M.

Bioinformatics. 2005 Jun;21 Suppl 1:i344-50.

PMID:
15961477
15.

Estimating trees from filtered data: identifiability of models for morphological phylogenetics.

Allman ES, Holder MT, Rhodes JA.

J Theor Biol. 2010 Mar 7;263(1):108-19. doi: 10.1016/j.jtbi.2009.12.001. Epub 2009 Dec 11.

PMID:
20004210
16.

Calibrating E-values for hidden Markov models using reverse-sequence null models.

Karplus K, Karchin R, Shackelford G, Hughey R.

Bioinformatics. 2005 Nov 15;21(22):4107-15. Epub 2005 Aug 25.

PMID:
16123115
17.

Using CLUSTAL for multiple sequence alignments.

Higgins DG, Thompson JD, Gibson TJ.

Methods Enzymol. 1996;266:383-402.

PMID:
8743695
18.

Maximum-scoring segment sets.

Csurös M.

IEEE/ACM Trans Comput Biol Bioinform. 2004 Oct-Dec;1(4):139-50.

PMID:
17051696
19.

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
20.

Non-hereditary Maximum Parsimony trees.

Fischer M.

J Math Biol. 2012 Aug;65(2):293-308. doi: 10.1007/s00285-011-0458-9. Epub 2011 Aug 13.

PMID:
21842167

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