Auden Cote-L'Heureux
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1ee6f5ceb6
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Small changes, see description
- Default partial filter cov threshold is 20%
- Changed script names
- Made requirement of conspecific names file explicit when using XPC
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2023-10-02 11:49:03 -04:00 |
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Auden Cote-L'Heureux
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b2e381e01d
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Typo fix
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2023-10-02 11:12:44 -04:00 |
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Auden Cote-L'Heureux
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4b934b8de2
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Rename 4_InFrameStopCodonEsimator.py to 4_InFrameStopCodonEstimator.py
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2023-10-02 11:11:49 -04:00 |
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Auden Cote-L'Heureux
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fa294909c5
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Updates to script 6 filters & script names
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2023-09-29 13:20:49 -04:00 |
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Auden Cote-L'Heureux
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f9d747ce38
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Delete PTL1/Transcriptomes/Scripts/7_FinalizeName.py
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2023-09-29 13:20:17 -04:00 |
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Auden Cote-L'Heureux
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5f28d4447f
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Delete PTL1/Transcriptomes/Scripts/6b_update_cov_post_removepartials.py
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2023-09-29 13:20:11 -04:00 |
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Auden Cote-L'Heureux
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eb3db88688
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Delete PTL1/Transcriptomes/Scripts/6_FilterPartials.py
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2023-09-29 13:20:05 -04:00 |
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Auden Cote-L'Heureux
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02ec29d737
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Delete PTL1/Transcriptomes/Scripts/5_GCodeTranslate.py
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2023-09-29 13:19:55 -04:00 |
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Auden Cote-L'Heureux
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0b6823d007
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Delete PTL1/Transcriptomes/Scripts/4_InFrameStopFreq.py
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2023-09-29 13:19:49 -04:00 |
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Auden Cote-L'Heureux
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6746899daa
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Delete PTL1/Transcriptomes/Scripts/3_CountOGsDiamond.py
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2023-09-29 13:19:43 -04:00 |
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Auden Cote-L'Heureux
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18981a792f
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Delete PTL1/Transcriptomes/Scripts/2b_remove_Bact.py
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2023-09-29 13:19:36 -04:00 |
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Auden Cote-L'Heureux
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b6f439e7d6
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Delete PTL1/Transcriptomes/Scripts/2a_remove_rRNA.py
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2023-09-29 13:19:30 -04:00 |
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Auden Cote-L'Heureux
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3e01100304
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Delete PTL1/Transcriptomes/Scripts/1b_XSpeciesContaminationAgnes.py
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2023-09-29 13:19:23 -04:00 |
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Auden Cote-L'Heureux
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67bbdd30b8
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Delete PTL1/Transcriptomes/Scripts/1a_ContigFiltStats.py
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2023-09-29 13:19:12 -04:00 |
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Adri K. Grow
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6a0b0ace3a
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Add files via upload
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2023-09-26 12:49:36 -04:00 |
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Auden Cote-L'Heureux
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032233968d
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Reverting to version of trees.py from before contamination loop work
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2023-09-18 12:58:48 -04:00 |
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Auden Cote-L'Heureux
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fe813b678d
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Delete PTL2/Scripts/trees.py
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2023-09-18 12:58:25 -04:00 |
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Auden Cote-L'Heureux
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7d54bb7416
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New script 6 with revised length filtration
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2023-09-18 10:06:36 -04:00 |
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Auden Cote-L'Heureux
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8ccb6eb9a7
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Delete PTL1/Transcriptomes/Scripts/6_FilterPartials.py
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2023-09-18 10:05:39 -04:00 |
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Auden Cote-L'Heureux
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106b2e2d89
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Added annotation to 4_CountOGsDiamond.py
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2023-09-18 10:04:25 -04:00 |
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Auden Cote-L'Heureux
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8e561dc735
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New Script 6 with fixed ciliate genetic code issue
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2023-09-18 10:02:48 -04:00 |
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Auden Cote-L'Heureux
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d300ade1b0
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Delete PTL1/Genomes/Scripts/6_SummaryStats.py
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2023-09-18 10:02:35 -04:00 |
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Auden Cote-L'Heureux
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3015aaa2eb
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New Script 4 with added Hook-relative length filter
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2023-09-18 10:02:06 -04:00 |
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Auden Cote-L'Heureux
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a45f921955
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Delete PTL1/Genomes/Scripts/4_CountOGsDiamond.py
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2023-09-18 10:01:44 -04:00 |
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Auden Cote-L'Heureux
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bceb9ff1de
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Delete PTL1/Genomes/Output directory
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2023-09-13 14:17:43 -04:00 |
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Auden Cote-L'Heureux
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8a2010d510
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Delete PTL1/Transcriptomes/Output directory
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2023-09-13 14:17:32 -04:00 |
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Adri K. Grow
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e502d2638f
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Add files via upload
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2023-09-01 14:35:08 -04:00 |
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Godwin Ani
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a7832842ae
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Fixed Tree script by Auden
Accepts both .fas and .fasta files now.
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2023-08-31 13:05:16 -04:00 |
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Godwin Ani
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7af603d7f4
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Delete PTL2/Scripts/trees.py
Script with .fas and .fasta issue.
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2023-08-31 13:04:18 -04:00 |
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Adri K. Grow
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c1b955d9b2
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Add files via upload
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2023-08-30 09:32:26 -04:00 |
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Adri K. Grow
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5d98dea9ff
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Delete run_phylotol.sh
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2023-08-30 09:31:58 -04:00 |
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Adri K. Grow
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c1d8ea93fc
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Add files via upload
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2023-08-30 09:29:33 -04:00 |
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Godwin Ani
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a60fb89a45
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output folder error solved
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2023-08-24 14:46:32 -04:00 |
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Auden Cote-L'Heureux
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13af646e65
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Small fix to ColorByClade_v2.0.py
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2023-08-22 10:00:11 -04:00 |
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Auden Cote-L'Heureux
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59f82e826c
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Small fix to 8_SummaryStats.py
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2023-08-21 13:25:04 -04:00 |
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Auden Cote-L'Heureux
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2f334642d3
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Small fix to 6_SummaryStats.py
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2023-08-21 13:24:42 -04:00 |
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Auden Cote-L'Heureux
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d4d1614e61
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Small fix to 6_SummaryStats.py
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2023-08-21 13:11:04 -04:00 |
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Auden Cote-L'Heureux
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b1bd9873af
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Adding date to stats summary script outputs
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2023-08-21 13:10:37 -04:00 |
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Auden Cote-L'Heureux
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37c1c36c7a
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Adding date to stat summary script
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2023-08-21 13:07:07 -04:00 |
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Auden Cote-L'Heureux
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f253022151
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Fixing 4-fold family error in CUB.py
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2023-08-21 12:47:45 -04:00 |
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Auden Cote-L'Heureux
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a24a546ade
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Fixing 4-fold family error in CUB.py
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2023-08-21 12:47:14 -04:00 |
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Auden Cote-L'Heureux
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42ff780332
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Fixing GC3-Degen calculation in CUB script
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2023-08-15 15:35:10 -04:00 |
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Auden Cote-L'Heureux
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3ec4cbfd63
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Delete CUB version with error (2.0)
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2023-08-15 15:34:46 -04:00 |
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Auden Cote-L'Heureux
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366e91256b
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Fixing line splitting bug in GuidanceWrapper_v2.1.py
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2023-08-14 15:01:54 -04:00 |
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Auden Cote-L'Heureux
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943bc3461d
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Adding allowance to backtranslating script for nucleotide sequences shorter than amino acid sequences by 3' trimming
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2023-08-10 10:40:19 -04:00 |
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Auden Cote-L'Heureux
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29daa4932b
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Small update to backtranslating script to account for sequence mismatch
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2023-08-10 10:33:34 -04:00 |
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Auden Cote-L'Heureux
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6324cabb71
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Adding first version of backtranslating script
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2023-08-10 10:24:50 -04:00 |
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Auden Cote-L'Heureux
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b08135e9b4
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Removing matplotlib dependency from 8_SummaryStats.py
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2023-08-04 15:05:10 -04:00 |
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Auden Cote-L'Heureux
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ab65eb7851
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Removing matplotlib requirement from 6_SummaryStats.py
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2023-08-04 14:29:50 -04:00 |
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Auden Cote-L'Heureux
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7223b4ee60
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Updating tree coloring script to fix rerooting issue and ease input customization
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2023-08-01 14:54:09 -04:00 |
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