dambe phylogenetics

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Results for dambe phylogenetics

1. Assessing substitution saturation with DAMBE - uOttawa

Aug 4, 2008 ... saturation with software DAMBE, which is a Windows program featuring a vari-
ety of analytical methods for molecular sequence analysis (Xia, 2001; Xia & Xie,.
2001). Substitution saturation decreases phylogenetic
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2. An index of substitution saturation and its application - uOttawa

genetic reconstruction of the simulated sequences when. NOTU equals 4, 8, or
16. The two phylogenetic methods yield essentially the same Ptrue values, and
only the neighbor-joining method is used for reconstructing to- pologies with

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3. DAMBE6: New Tools for Microbial Genomics, Phylogenetics, and

Apr 4, 2017 ... Abstract. DAMBE is a comprehensive software workbench for data analysis in
molecular biology, phylogenetics, and evolution. Several important new functions
have been added since version 5 of. DAMBE: 1)
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4. DAMBE: Software Package for Data Analysis in - Oxford Academic

Aug 16, 2000 ... and jackknifing, significance tests of mo- lecular clock and alternative
phylogenetic hypotheses (i.e., how much better is the best tree compared to
alternative trees), fitting statistical distributions to substitu
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5. The Phylogenetic Handbook - EVA UdelaR

and phylogeny software, including Blast, FastA, Clustal, T-coffee, Muscle, Dambe
, Tree-Puzzle,. Phylip, Mega4,Paup*, Iqpnni, Consel,ModelTest,ProtTest, Paml,
HyPhy, MrBayes,Beast,Lamarc,. SplitsTree, and Rdp3. Many analysis tools a
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6. Chapter 21 Testing Phylogenetic Hypotheses - Springer Link

This of course would increase the difficulty to reject a null hypothesis, even if the
null hypothesis is false. The Student-Newman-Keuls test is appropriate for
significance test involving multiple comparisons. It is used in DAMBE for all
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7. A Comprehensive Software Package for Data - Semantic Scholar

and is freely available from http://dambe.bio.uottawa.ca (last accessed April 16,
2013). Key words: bioinformatics, phylogenetics, dating, Gibbs sampler, motif
discovery, secondary structure, codon usage, hidden Markov model, genom
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8. The Phylogenetic Handbook - Semantic Scholar

The Phylogenetic Handbook: a Practical Approach to Phylogenetic Analysis and
Hypothesis Testing,. Philippe Lemey ... in retrieving the correct phylogenetic tree
depends on how well any particular data set meets such ...... (
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9. Part I. Molecular phylogenetics, and phylogeny-based comparative

Mar 8, 2013 ... phylogenetic reconstruction, by using distance-based methods, with the
sequences we align in this lab. Procedures. Download the COII.FAS file from http
://dambe.bio.uottawa.ca/download.asp and save it to your
Tags:dambe phylogenetics

10. The impact of sequence parameter values on phylogenetic accuracy

impact of some features of nucleotide sequences in alignments on phylogenetic (
topological) accuracy rather than any source of error during the ..... distance (Xia
and Xie 2001). A more sophisticated method is the entropy-based test of Tags:dambe phylogenetics

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