# Plot Multiple Sequence Alignment using 'ggplot2'

## Documentation for package ‘ggmsa’ version 1.0.2

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

## Help Pages

available_colors | List Color Schemes currently available
available_fonts | List Font Families currently available
available_msa | List MSA objects currently available
color_Clustal | A color scheme of Culstal. The algorithm to assign colors for Multiple Sequence.
color_scheme | Assigning colors to sequence alignment.
facet_msa | segment MSA
geom_GC | geom_GC
geom_helix | geom_helix
geom_msa | geom_msa
geom_msaBar | geom_msaBar
geom_seed | geom_seed
geom_seqlogo | geom_seqlogo
get_consensus | calling the consensus sequence.
gghelix | gghelix
ggmsa | ggmsa
ggSeqBundle | ggSeqBundle
msa2tidy | This function converts the msa_data to the tidy data.
plot | plot method for SeqDiff object
plot-method | plot method for SeqDiff object
readSSfile | readSSfile
seqdiff | seqdiff
SeqDiff-class | show method
seqlogo | seqlogo
show | show method
show-method | show method
simplot | simplot
tidy_color | cleaning the needless sequeces' color according to the consensus sequcence (only used in the consensus views).
tidy_msa | tidy_msa