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Items: 1 to 20 of 95

1.

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. doi: 10.1186/1471-2148-8-317. Erratum in: BMC Evol Biol. 2009;9:200. doi:10.1186/1471-2148-9-200.

2.

Phylogenetic tree reconstruction accuracy and model fit when proportions of variable sites change across the tree.

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

Syst Biol. 2010 May;59(3):288-97. doi: 10.1093/sysbio/syq003. Epub 2010 Mar 1.

3.

Mixture models of nucleotide sequence evolution that account for heterogeneity in the substitution process across sites and across lineages.

Jayaswal V, Wong TK, Robinson J, Poladian L, Jermiin LS.

Syst Biol. 2014 Sep;63(5):726-42. doi: 10.1093/sysbio/syu036. Epub 2014 Jun 12.

PMID:
24927722
4.

A mixed branch length model of heterotachy improves phylogenetic accuracy.

Kolaczkowski B, Thornton JW.

Mol Biol Evol. 2008 Jun;25(6):1054-66. doi: 10.1093/molbev/msn042. Epub 2008 Mar 3.

5.
7.

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. doi: 10.1186/1471-2148-8-331.

9.

Testing for covarion-like evolution in protein sequences.

Wang HC, Spencer M, Susko E, Roger AJ.

Mol Biol Evol. 2007 Jan;24(1):294-305. Epub 2006 Oct 20.

10.

A gamma mixture model better accounts for among site rate heterogeneity.

Mayrose I, Friedman N, Pupko T.

Bioinformatics. 2005 Sep 1;21 Suppl 2:ii151-8.

11.

CSMET: comparative genomic motif detection via multi-resolution phylogenetic shadowing.

Ray P, Shringarpure S, Kolar M, Xing EP.

PLoS Comput Biol. 2008 Jun 6;4(6):e1000090. doi: 10.1371/journal.pcbi.1000090.

13.

Correlated evolution of nucleotide substitution rates and allelic variation in Mhc-DRB lineages of primates.

Garamszegi LZ, de Groot NG, Bontrop RE.

BMC Evol Biol. 2009 Apr 12;9:73. doi: 10.1186/1471-2148-9-73.

14.

Difficulties in testing for covarion-like properties of sequences under the confounding influence of changing proportions of variable sites.

Gruenheit N, Lockhart PJ, Steel M, Martin W.

Mol Biol Evol. 2008 Jul;25(7):1512-20. doi: 10.1093/molbev/msn098. Epub 2008 Apr 18.

15.

NETGEN: generating phylogenetic networks with diploid hybrids.

Morin MM, Moret BM.

Bioinformatics. 2006 Aug 1;22(15):1921-3. Epub 2006 May 22.

16.
17.

A nonparametric method for accommodating and testing across-site rate variation.

Huelsenbeck JP, Suchard MA.

Syst Biol. 2007 Dec;56(6):975-87.

PMID:
18075934
18.

A method for detecting positive selection at single amino acid sites.

Suzuki Y, Gojobori T.

Mol Biol Evol. 1999 Oct;16(10):1315-28.

19.

Towards realistic codon models: among site variability and dependency of synonymous and non-synonymous rates.

Mayrose I, Doron-Faigenboim A, Bacharach E, Pupko T.

Bioinformatics. 2007 Jul 1;23(13):i319-27.

20.
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