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JLSteenwyk
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ClipKIT
a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference
https://jlsteenwyk.com/ClipKIT/
MIT License
61
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Bump setuptools from 69.5.1 to 70.0.0
#58
dependabot[bot]
opened
2 months ago
0
Bump zipp from 3.1.0 to 3.19.1
#57
dependabot[bot]
opened
2 months ago
0
Bump certifi from 2023.7.22 to 2024.7.4
#56
dependabot[bot]
opened
2 months ago
0
Bump urllib3 from 1.26.4 to 1.26.19 in /docs
#55
dependabot[bot]
opened
3 months ago
0
Bump tornado from 6.1 to 6.4.1 in /docs
#54
dependabot[bot]
opened
3 months ago
0
Bump requests from 2.23.0 to 2.32.0
#53
dependabot[bot]
opened
4 months ago
0
Bump jinja2 from 2.11.3 to 3.1.4 in /docs
#52
dependabot[bot]
opened
5 months ago
0
Bump tqdm from 4.66.2 to 4.66.3
#51
dependabot[bot]
opened
5 months ago
0
Bump idna from 2.10 to 3.7 in /docs
#50
dependabot[bot]
closed
5 months ago
1
Bump certifi from 2020.4.5.1 to 2023.7.22
#49
dependabot[bot]
closed
5 months ago
0
fixed errors that were throwing errors for docs
#48
JLSteenwyk
closed
5 months ago
0
Added support for Python 3.11
#47
JLSteenwyk
closed
5 months ago
0
Cannot Install the clipkit
#46
zhangwenda0518
closed
5 months ago
1
remove gaps and codon[YYYY-MM-DD]: [BUG TITLE]
#45
nbat64
closed
6 months ago
9
added cst mode of trimming
#44
JLSteenwyk
closed
6 months ago
0
Question about clarifying defaults for --gap_characters
#43
smorzechowski
closed
7 months ago
2
Enable codon option in programmatic interface
#42
TJBIII
closed
8 months ago
0
Code used to benchmark
#41
sen-pai
closed
8 months ago
1
2023-12-05: Difference between parameters `smart-gap`, `gappy` and `kpic-gappy`
#40
sanyalab
closed
10 months ago
3
[2023-12-05]: Cannot Install latest version of clipkit
#39
sanyalab
closed
10 months ago
2
Change to trimming behavior with gappyness threshold?
#38
chtsai0105
closed
1 year ago
2
Numpy performance improvements
#37
TJBIII
closed
1 year ago
0
2023-08-24: Use numpy to accelerate the trimming process
#36
chtsai0105
closed
1 year ago
2
Bump certifi from 2020.12.5 to 2023.7.22 in /docs
#35
dependabot[bot]
closed
1 year ago
1
Add tests for api module
#34
TJBIII
closed
1 year ago
0
Bump pygments from 2.7.4 to 2.15.0
#33
dependabot[bot]
closed
1 year ago
1
Bump requests from 2.23.0 to 2.31.0
#32
dependabot[bot]
closed
1 year ago
1
Dev ClipKIT 2.0
#31
JLSteenwyk
closed
1 year ago
0
Bump requests from 2.25.1 to 2.31.0 in /docs
#30
dependabot[bot]
closed
1 year ago
1
Should I make consensus sequence before using Clipkit or after ClipKit
#29
Rohit-Satyam
closed
1 year ago
3
Bump certifi from 2020.4.5.1 to 2022.12.7
#28
dependabot[bot]
closed
1 year ago
1
added to change log for 1.4.0 in docs
#27
JLSteenwyk
closed
1 year ago
0
Seq type handling
#26
JLSteenwyk
closed
1 year ago
0
extract parsimony sites
#25
atongsa
closed
1 year ago
1
Refactor stats calculation and return stats from execute
#24
TJBIII
closed
1 year ago
0
Bump certifi from 2020.12.5 to 2022.12.7 in /docs
#23
dependabot[bot]
closed
1 year ago
1
Bump numpy from 1.18.2 to 1.21.0
#22
dependabot[bot]
closed
2 years ago
0
Bump numpy from 1.18.2 to 1.21.0 in /docs
#21
dependabot[bot]
closed
2 years ago
0
Preserve sequence description for FASTA
#20
edgardomortiz
closed
2 years ago
2
Trim CDS sequence
#19
jsharbrough
closed
2 years ago
4
Bump babel from 2.9.0 to 2.9.1 in /docs
#18
dependabot[bot]
closed
2 years ago
1
Bump py from 1.8.1 to 1.10.0 in /docs
#17
dependabot[bot]
closed
2 years ago
0
on pinning dependency versions
#16
ialbert
closed
2 years ago
2
resulting trimmed alignment not printed to specified output file (-o) when also using -log
#15
jolienvanhooff
closed
3 years ago
6
Output sequence as digits
#14
andersgs
closed
3 years ago
6
Bump urllib3 from 1.26.4 to 1.26.5 in /docs
#13
dependabot[bot]
closed
3 years ago
1
Bump pygments from 2.6.1 to 2.7.4
#12
dependabot[bot]
closed
3 years ago
0
Bump py from 1.8.1 to 1.10.0
#11
dependabot[bot]
closed
3 years ago
0
help message
#10
haruosuz
closed
3 years ago
1
Bump pygments from 2.6.1 to 2.7.4 in /docs
#9
dependabot[bot]
closed
3 years ago
2
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