aa2d7b52ae39003820455af9a030031e *DESCRIPTION
47e71a08753983dae80170cd3f31c5bd *NAMESPACE
2fe648f16faad463536605a5c818ecc7 *NEWS.md
4e0bbeacefc74afd695314437f40c825 *R/AllClasses.R
919d5d82c23e2f447ee70bb5c5c02f06 *R/SeqBundles.R
e631b91d9c91b46ba32c9f54907e435c *R/ancestor_seq.R
1fdfca65a3116e08c1fba4f3eb6eed22 *R/arc.R
cde8f4c4d94c7e73d15b7da8b86754d4 *R/available.R
a79cd1dcc3c95c209858f655a94d9621 *R/clustal.R
352888478181e7b426acbd91efa650ec *R/color_by_conservation.R
0685529468a698796ccd4a81eb7bf332 *R/color_else.R
e009e29951215dc05af4e4ae2fef16ac *R/cons.R
34301713f8287aefd609b7f4a293a130 *R/data.R
457f48dea4d6d21792c88ec32801ec4e *R/dms.R
77240455590862c63b61f91f712aa4b3 *R/facet_msa.R
48136c30ff2ae4038de90c235e1579db *R/geom_GC.R
5588f811e9b2fc40778b2d38acc7c3c3 *R/geom_asterisk.R
8b02bad013c5f8db3e3769aeb5c7056c *R/geom_msa.R
45d174f5d0c003d01c4ca5e435b4df1d *R/geom_msaBar.R
9cf5db7aa9b5e4390cc4931687447c03 *R/geom_seed.R
c6829ff777ce72e0804c99b9c1c62ee7 *R/ggmaf.R
01ef7f2e7f06ee25babd28ebb15939e7 *R/ggmsa.R
e618934675e27afb23bfb68c45fed9d6 *R/import-functions.R
7950d4c28d1444e08f3c4c7b3b09c2e5 *R/method-plot.R
47bef0ba3131968a7d4d9eb9b028b069 *R/method-show.R
adc96b67e46f923629f3059bd445b363 *R/methods-diff.R
af099f5e41c3b1f2e1aeac52ffc73450 *R/methods-ggplot_add.R
aa338d703fa7b9f7156204f7349096ee *R/msa_data.R
fe31c912b47e038353f052d2e9f77f6e *R/pp_interactive.R
f003fcc52fa846c058c814f3ddcb9c68 *R/prepare_fasta.R
7e795e72bd0b48af6b3008ad9f16b20b *R/read_maf.R
8854bdbaa9f0680b9cb88b94635d7c1d *R/seqdiff.R
9b6e61265aa3dfb340b3bee0d1c07dcf *R/seqlogo.R
dd8a15041042372e8e07ebc28071362b *R/simplot.R
1312bf1d52fbeaabee714cde7a525a08 *R/sysdata.rda
ea059a2b707a2d0393afa03a6cc8d3d2 *R/theme_msa.R
7cb8bf6a4607f9bc4b870edfde04621b *R/zzz.R
8fccaa4002a23c027694afa04f9dca12 *build/vignette.rds
fc842db9d8632e18df2477512a3aaf83 *inst/CITATION
13ca781e9888ab9b72fb1583fd84a737 *inst/doc/ggmsa.R
d60fcef481cdfeca78784d4d68fddb97 *inst/doc/ggmsa.Rmd
2fbd60d92dce17d70fcbf37c25cf2465 *inst/doc/ggmsa.html
d46d5ba53d2a3511b65a79e2f6635ad5 *inst/extdata/GVariation/A.Mont.fas
437ae9572cb3161f8bb4ea9ac59ccf66 *inst/extdata/GVariation/B.Oz.fas
011e3b9f9cb0a09da738e97e4bc3d6c0 *inst/extdata/GVariation/C.Wilga5.fas
d8b7a8e099688562ffa607afa0fd4ad2 *inst/extdata/GVariation/sample_alignment.fa
c0182cf537c609599cbf71ce23670608 *inst/extdata/Gram-negative_AKL.fasta
4766763d96e1e0ff55b1cc7b2900d4ae *inst/extdata/Gram-positive_AKL.fasta
283d3781ddd4ec3839743d1c13f11bce *inst/extdata/LeaderRepeat_All.fa
83c0d3f3b06dd3cbde5fd59388189042 *inst/extdata/Rfam/RF00458.fasta
4dbf1918d97f7dc999bff960dd77487d *inst/extdata/Rfam/RF03120.fasta
c659e072962d2ab1f396753764767d48 *inst/extdata/Rfam/RF03120_SS.txt
7b18b0240dc892042b9ee3eef87e31ce *inst/extdata/TP53_genes.xlsx
4d4900e66d223093ed5d8fcbd408ddf8 *inst/extdata/sample.fasta
cc4275de9362bd471e0fc02b9755d510 *inst/extdata/seedSample.fa
a332af24853c5ee0f7f84d2eda203337 *inst/extdata/sequence-link-tree.fasta
89165b84dada3df8702f1d0b4809e1da *inst/extdata/tp53.fa
1b728966b7df0f548240590316476e2a *man/GVariation.Rd
2cce85eb6de4111c67f4dccfe2db3bb8 *man/Gram-negative_AKL.fasta.Rd
7317f5b3daec0be8547f325a4a70ca88 *man/Gram-positive_AKL.fasta.Rd
f5c9f01a9d8bf22bb52e908cae22b45b *man/LeaderRepeat_All.fa.Rd
5589c2a22f5b4ec7727901544ee8f912 *man/Rfam.Rd
7e461d0084358c46eddca7ff739e4f6e *man/TP53_genes.xlsx.Rd
eaefb1bf6bbaecbefed778a0e43a3d80 *man/adjust_ally.Rd
3872635a5210365a67171de603e5f763 *man/assign_dms.Rd
786a3ae4cdb53ed1929d31a640229425 *man/available_colors.Rd
39584fd243738a03d58c0460ae7880db *man/available_fonts.Rd
2fea7d12f44a3d930305b2248883a8c7 *man/available_msa.Rd
ed3415073d63d3edb6deaad67523d417 *man/extract_seq.Rd
b8afa47bc67629a44a027e727ae5ad70 *man/facet_msa.Rd
620015533a975e96af0348720e631c2d *man/figures/REAMED-unnamed-chunk-6-1.png
cfe29534bccc344345caa5f45d0f53b3 *man/geom_GC.Rd
55153d4ea7e669a4cc8481978fa33dd5 *man/geom_helix.Rd
3f848ec15dcf5320afae84b3d12cb7c4 *man/geom_msa.Rd
93751da4d2adfcd2aae559a58c5e3e2a *man/geom_msaBar.Rd
7fd32fa1f471b6aba6e41dbfaf2fdfb0 *man/geom_seed.Rd
5affff64a624accb07771065500b7f65 *man/geom_seqlogo.Rd
22c307473c6b5c31a86d1bcb47919999 *man/ggSeqBundle.Rd
882c0160cb4e7bfbb5b3bce60b52f996 *man/gghelix.Rd
3cd82b8d93cc2aacc6b489737a00c1f2 *man/ggmaf.Rd
0692c51205bd4f295f4d7893fedd1d71 *man/ggmsa.Rd
cf85597877a78f22796e3715dd5d0de5 *man/merge_seq.Rd
d785ddec8b620e67b1d7da75958373c9 *man/plot-methods.Rd
235f1dbbe08048bf79e5fc0c548d0329 *man/readSSfile.Rd
914ab612229a6f79073321993ab20fb2 *man/read_maf.Rd
2b23e766d1784ae06a78da185850ac3d *man/reset_pos.Rd
70b3c537d1ebf9814b4f84a50bda3b13 *man/sample.fasta.Rd
df842eb88b46122615fdf83b8272d92b *man/seedSample.fa.Rd
b1f14c104b495a7c31f7b24a854bc2ff *man/seqdiff.Rd
786c7b5d35e6f1df86387d5924eb76e1 *man/seqlogo.Rd
2114fcbe114a711f22a2a919a5a315e8 *man/sequence-link-tree.fasta.Rd
f7327ea7e879c615c9522e2c954f7acb *man/show-methods.Rd
d0ac7b2fb20949c3f06a293da831489a *man/simplify_hdata.Rd
a5f4d2eb4be47627c65a2f412e680a29 *man/simplot.Rd
6b48278ee1d2f7f004ee106ea49a8c4b *man/theme_msa.Rd
6b3662f1c607b7cdd60c79b515e21297 *man/tidy_hdata.Rd
6d66f30c3d419b553b88bb0aa0c6362c *man/tidy_maf_df.Rd
3f05a5c2acf57c40d5bb5c75c6538d52 *man/tidy_msa.Rd
8573107ec7f3a4f930e96a4a662cceab *man/tp53.fa.Rd
b0f076cccd0f8adf6e8603eff3f44d14 *man/treeMSA_plot.Rd
d9d1020b5ebc1747215c344b928ad71a *tests/testthat.R
239c0367aad9abb059a45f40c36a0d80 *tests/testthat/test-main.R
a391ac60a1cb602b57223736398592da *tests/testthat/test-msa_data.R
fd044fcefc180afd17f4c80af3a971ec *tests/testthat/test-tidy_msa.R
d60fcef481cdfeca78784d4d68fddb97 *vignettes/ggmsa.Rmd
5088a6efb7bd219ddc9c35b2abb378eb *vignettes/ggmsa.bib
984174170b02a9fdf7d4e9f6c03d2de0 *vignettes/man/figures/schemes.png
3734a7ebdaca5b9aa002158e4d8c9488 *vignettes/man/figures/workflow.png
