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


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Documentation for package ‘sitePath’ version 1.0.3

Help Pages

addMSA Prepare data for sitePath analysis
extractTips Extract sitePath for a single site
extractTips.fixationSites Extract sitePath for a single site
extractTips.multiFixationSites Extract sitePath for 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
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
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