# Detection of sites with fixation of amino acid substitutions in protein evolution

## Documentation for package ‘sitePath’ version 1.4.2

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

addMSA | Prepare data for sitePath analysis
extractSite | Extract info for fixation of a single site
extractSite.fixationSites | Extract info for fixation of a single site
extractSite.multiFixationSites | Extract info for fixation of a single site
extractTips | Extract info for fixation of a single site
extractTips.fixationSites | Extract info for fixation of a single site
extractTips.multiFixationSites | Extract info for fixation of a single site
extractTips.sitePath | Extract info for fixation of a single site
findSites | Finding sites with variation
fixationSites | Finding sites with variation
fixationSites.lineagePath | Finding sites with variation
groupTips | Topology-dependent tree trimming
h3n2_align | Multiple sequence alignment of H3N2's HA protein
h3n2_align_reduced | Truncated data for runnable example
h3n2_tree | Phylogenetic tree of H3N2's HA protein
h3n2_tree_reduced | Truncated data for runnable example
lineagePath | Topology-dependent tree trimming
multiFixationSites | Finding sites with variation
multiFixationSites.lineagePath | Finding sites with variation
plot.lineagePath | Visualize phylogenetic lineages
plot.sitePath | Plot the fixation mutation
plotSingleSite | Color the tree by a single site
plotSingleSite.fixationSites | Color the tree by a single site
plotSingleSite.lineagePath | Color the tree by a single site
plotSingleSite.multiFixationSites | Color the tree by a single site
pre-assessment | Things can be done before the analysis
setSiteNumbering | Set site numbering to the reference sequence
setSiteNumbering.lineagePath | Set site numbering to the reference sequence
setSiteNumbering.phylo | Set site numbering to the reference sequence
similarityMatrix | Things can be done before the analysis
sneakPeek | Things can be done before the analysis
SNPsites | Finding sites with variation
treemer | Topology-dependent tree trimming
zikv_align | Multiple sequence alignment of Zika virus polyprotein
zikv_align_reduced | Truncated data for runnable example
zikv_tree | Phylogenetic tree of Zika virus polyprotein
zikv_tree_reduced | Truncated data for runnable example