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‎docs/05-alignment.md‎

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@@ -105,7 +105,7 @@ DNA.no_trans <- AlignSeqs(dna)
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## Aligning Sequences:
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## ================================================================================
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## Realigning Sequences:
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## Realigning Sequences:
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```
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Translating the nucleotide sequences sped up the alignment process, although both were fast enough it isn't a big deal to directly align the nucleotides. Your choice of which alignment procedure to use will largely come down to whether you are using coding sequence and how divergent your samples are. If you aren't using coding sequence, you will need to align using the nucleotides. If you have samples from deeply divergent species (especially if they come from different phyla), you will generally get a better alignment if you let the program translate your nucleotide sequence to amino acids first.
@@ -264,7 +264,7 @@ DNA.no_trans.1 <- AlignSeqs(dna, gapOpening = c(-20, -10), gapExtension = c(-5,
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‎docs/06-neighbor-joining.md‎

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## Realigning Sequences:
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‎docs/09-maximum-likelihood.md‎

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## unconstrained loglikelihood: -20944.97
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## Discrete gamma model
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## Number of rate categories: 4
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## Rate matrix:
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## model: GTR+G(4)+I
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## loglikelihood: -11945.78
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## unconstrained loglikelihood: -20944.97
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## Proportion of invariant sites: 5.218685e-05
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## Proportion of invariant sites: 5.218644e-05
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## Discrete gamma model
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## Shape parameter: 1.196526
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## c 0.4369734 0.0000000 0.4602445 2.7015575
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## g 1.6803296 0.4602445 0.0000000 1.0000000
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## model: K80+I
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## loglikelihood: -12195.32
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‎docs/11-time-trees.md‎

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```
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‎docs/404.html‎

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‎docs/About.md‎

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## collate en_US.UTF-8
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## pandoc 3.1.1 @ /usr/local/bin/ (via rmarkdown)
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‎docs/about-the-authors.html‎

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‎docs/adding-calibration-points-to-your-phylogenies.html‎

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<pre><code>##
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<p>Before we plot the tree, we need to do a bit of formatting of the branch lengths (called edge.length). R will be default save these values to 10 decimal places, which can make visualization a little tricky. We’re going to format them so they only have two decimal places, then plot them on top of the time tree.</p>
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<div class="sourceCode" id="cb141"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb141-1"><a href="adding-calibration-points-to-your-phylogenies.html#cb141-1" tabindex="-1"></a>time.tree_dated<span class="sc">$</span>edge.length <span class="ot">&lt;-</span> <span class="fu">round</span>(time.tree_dated<span class="sc">$</span>edge.length, <span class="at">digits =</span> <span class="dv">2</span>)</span>

‎docs/ancestral-state-reconstruction.html‎

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‎docs/building-a-neighbor-joining-tree.html‎

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