YuLab-SMU/ggmsa

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:traffic_light: Visualizing publication-quality multiple sequence alignment using ggplot2

Stars: 220
Forks: 28
Open beginner issues: 0
Indexed issues: 53

Dominant language: R
License: No license data
Last GitHub push: Jun 9, 2026
Latest indexed: Sep 21, 2026
Contributing guide: No contributing guide
Code of conduct: No code of conduct
Beginner labels: No beginner labels indexed
PR merge metrics: No merged PRs in 30d

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45 open issues indexed

Some color schemes make black text hard to read. suggestion: adaptive text color Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

YuLab-SMU/ggmsa#73 · Opened Jan 16, 2026
facet_msa creates breaks in the graph and tiles are not square Open

Difficulty 3/5 1-2 days Newbie friendliness 38/100

YuLab-SMU/ggmsa#72 · Opened Sep 26, 2025
Needing more flexible parameter/argument adjustment of geom_seqlogo() Open

Difficulty 2/5 1-3 hours Newbie friendliness 55/100

YuLab-SMU/ggmsa#71 · Opened Sep 11, 2025
Adding amino acid annotations Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

YuLab-SMU/ggmsa#70 · Opened Jul 31, 2024
Add overlay for Domains and other annotations Open

Difficulty 5/5 Over a week Newbie friendliness 35/100

YuLab-SMU/ggmsa#67 · Opened Apr 25, 2024
ggmsa函数可能需要一个选择比对序列类型的参数 Open

Difficulty 4/5 3-5 days Newbie friendliness 32/100

YuLab-SMU/ggmsa#66 · Opened Apr 3, 2024
ggmsa rlang error Open

Difficulty 3/5 1-2 days Newbie friendliness 42/100

YuLab-SMU/ggmsa#64 · Opened Feb 8, 2024
Consensus Sequence Threshold? Open

Difficulty 2/5 1-3 hours Newbie friendliness 25/100

YuLab-SMU/ggmsa#63 · Opened Oct 30, 2023
Support alignments from `msa` package Open

Difficulty 3/5 1-2 days Newbie friendliness 45/100

YuLab-SMU/ggmsa#61 · 2 reactions · Opened Aug 3, 2023
How to shift to display the conservative region, and separates the mismatched regions？ Open

Difficulty 5/5 Over a week Newbie friendliness 20/100

YuLab-SMU/ggmsa#60 · Opened Aug 1, 2023
Seq names are not shown Open

Difficulty 3/5 1-2 days Newbie friendliness 45/100

YuLab-SMU/ggmsa#59 · Opened Jun 22, 2023
adjusting geom_msabar() Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

YuLab-SMU/ggmsa#57 · Opened Apr 12, 2023
Plotting alignment in wide format Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

YuLab-SMU/ggmsa#56 · 1 comment · 4 reactions · Opened Feb 20, 2023
boxshade color Open

Difficulty 4/5 3-5 days Newbie friendliness 30/100

YuLab-SMU/ggmsa#55 · Opened Feb 16, 2023
Error in parse(text = elt) : <text>:1:7: unexpected symbol Open

Difficulty 3/5 1-2 days Newbie friendliness 25/100

YuLab-SMU/ggmsa#53 · 2 comments · Opened Oct 14, 2022
ggmsa is very slow cause of a very big pdf? Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

YuLab-SMU/ggmsa#52 · 2 reactions · Opened Aug 17, 2022
Text overlapping. Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

YuLab-SMU/ggmsa#48 · 2 comments · Opened Jul 25, 2022
Protein secondary structure & domain annotation Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

YuLab-SMU/ggmsa#47 · 6 comments · Opened Jul 19, 2022
The ggmsa::ggSeqBundle() of arg:line_widch should be line_width? Open

Difficulty 1/5 Under an hour Newbie friendliness 25/100

YuLab-SMU/ggmsa#44 · Opened Jul 1, 2022
Creat FASTA files from APE files Open

Difficulty 5/5 Over a week Newbie friendliness 20/100

YuLab-SMU/ggmsa#43 · 1 comment · 1 reaction · Opened Jun 23, 2022
Is there a way to only highlight/colour unconserved regions? Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

YuLab-SMU/ggmsa#42 · 2 comments · Opened Jun 5, 2022
how to add a group of point in to ggmsa Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

YuLab-SMU/ggmsa#41 · 1 comment · Opened May 31, 2022
Font in alignments is pixelated Open

Difficulty 4/5 3-5 days Newbie friendliness 30/100

YuLab-SMU/ggmsa#37 · 3 comments · Opened May 13, 2022
Error in if (freq1 > 0.9 && freq2 > 0) {: missing value where TRUE/FALSE needed Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

YuLab-SMU/ggmsa#36 · 1 comment · Opened May 13, 2022
Note: wrong number of arguments to 'seq_len' Open

Difficulty 3/5 1-2 days Newbie friendliness 25/100

YuLab-SMU/ggmsa#35 · 2 comments · Opened May 13, 2022
How to install ggmsa under R 3.6 Open

Difficulty 4/5 3-5 days Newbie friendliness 20/100

YuLab-SMU/ggmsa#33 · 3 comments · Opened May 5, 2022
Add a 'None' option for color Open

Difficulty 2/5 1-3 hours Newbie friendliness 72/100

YuLab-SMU/ggmsa#32 · 4 comments · Opened Feb 4, 2022
Geom_Logo masks the first line of sequence alignment Open

Difficulty 3/5 1-2 days Newbie friendliness 42/100

YuLab-SMU/ggmsa#28 · 5 comments · Opened Dec 4, 2021
Problems with tree, MSA and logo Open

Difficulty 4/5 3-5 days Newbie friendliness 30/100

YuLab-SMU/ggmsa#27 · 2 comments · Opened Dec 2, 2021
Adjusting x axis of facet_msa? Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

YuLab-SMU/ggmsa#26 · 3 comments · Opened Nov 25, 2021
ggmsa plot error due to unique names Open

Difficulty 3/5 1-2 days Newbie friendliness 30/100

YuLab-SMU/ggmsa#25 · 4 comments · Opened Nov 24, 2021
I can't find Cripavirus.fasta Open

Difficulty 2/5 1-3 hours Newbie friendliness 35/100

YuLab-SMU/ggmsa#24 · 2 comments · Opened Nov 22, 2021
Combine ggmsa plot and ggtree? Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

YuLab-SMU/ggmsa#23 · 2 comments · Opened Nov 9, 2021
Annotating a specific facet Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

YuLab-SMU/ggmsa#20 · 4 comments · Opened Jun 24, 2021
Error in .Call2 with DNAbin Open

Difficulty 3/5 1-2 days Newbie friendliness 25/100

YuLab-SMU/ggmsa#19 · 3 comments · Opened Mar 31, 2021
print on several pages Open

Difficulty 5/5 Over a week Newbie friendliness 28/100

YuLab-SMU/ggmsa#17 · 2 comments · Opened Jan 23, 2021
Sorry，But I ggmsa picture is grey！ Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

YuLab-SMU/ggmsa#15 · 17 comments · Opened Dec 22, 2020
Possible to create custom colour schemes? Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

YuLab-SMU/ggmsa#14 · 4 comments · Opened Dec 17, 2020
Last row of facet_msa has different width characters Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

YuLab-SMU/ggmsa#13 · 3 comments · Opened Dec 8, 2020
`Chemistry_AA` color showing even when `color` parameter is set to `Clustal` Open

Difficulty 3/5 1-2 days Newbie friendliness 45/100

YuLab-SMU/ggmsa#12 · Opened Oct 29, 2020
geom_seqlogo + facet_msa Open

Difficulty 3/5 1-2 days Newbie friendliness 42/100

YuLab-SMU/ggmsa#11 · Opened Sep 3, 2020
Feature Request: Consensus View Open

Difficulty 5/5 Over a week Newbie friendliness 32/100

YuLab-SMU/ggmsa#10 · 8 comments · Opened Sep 2, 2020
could not find function "geom_facet" Open

Difficulty 3/5 1-2 days Newbie friendliness 42/100

YuLab-SMU/ggmsa#6 · 1 comment · Opened Apr 24, 2020
How is it broken down? Open

YuLab-SMU/ggmsa#5 · 2 comments · 1 assignee · Opened Apr 18, 2020
add star under special sequence automatically, eg. miRNA seed Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

YuLab-SMU/ggmsa#4 · 1 comment · Opened Oct 8, 2019

YuLab-SMU/ggmsa

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