# Plot Multiple Sequence Alignment using 'ggplot2'

## Documentation for package ‘ggmsa’ version 1.4.0

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

## Help Pages

adjust_ally | adjust_ally
assign_dms | assign_dms
available_colors | List Color Schemes currently available
available_fonts | List Font Families currently available
available_msa | List MSA objects currently available
extract_seq | extract_seq
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
gghelix | gghelix
ggmaf | ggmaf
ggmsa | ggmsa
ggSeqBundle | ggSeqBundle
Gram-negative_AKL.fasta | Gram-negative_AKL
Gram-positive_AKL.fasta | Gram-positive_AKL
GVariation | GVariation
LeaderRepeat_All.fa | A sample DNA alignment sequences
merge_seq | merge_seq
plot | plot method for SeqDiff object
plot-method | plot method for SeqDiff object
readSSfile | readSSfile
read_maf | read_maf
reset_pos | reset_pos
Rfam | Rfam
sample.fasta | A sample data used in ggmsa
seedSample.fa | microRNA data used in ggmsa
seqdiff | seqdiff
SeqDiff-class | show method
seqlogo | seqlogo
sequence-link-tree.fasta | sequence-link-tree
show | show method
show-method | show method
simplify_hdata | simplify_hdata
simplot | simplot
theme_msa | theme_msa
tidy_hdata | tidy_hdata
tidy_maf_df | tidy_maf_df
tidy_msa | tidy_msa
tp53.fa | TP53 MSA
TP53_genes.xlsx | genome locus
treeMSA_plot | treeMSA_plot