72 Commits

Author	SHA1	Message	Date
Adri K. Grow	20d3926f10	Update CladeGrabbing.py ... Adding new optional arguments to support two-step clade filtering within one run of the script.	2025-08-18 10:54:25 -04:00
Adri K. Grow	586a9e0c63	Update CladeGrabbing.py	2025-07-08 07:54:58 -04:00
Katzlab	aec7f6caf9	Update ColorByClade.py ... Changed to root on bacteria (Ba) and not prokaryotes (Ba, Za).... did not test	2025-07-01 16:18:54 -04:00
Godwin N. Ani	d7577022c4	Update CladeSizes.py	2025-03-24 15:01:48 -04:00
Godwin Ani	45de3036c9	Update ShortenTips.py	2025-02-04 18:59:31 -05:00
Godwin Ani	7e9b90c79b	Shorten tree tip names	2025-02-04 18:58:53 -05:00
Auden Cote-L'Heureux	a8a2a5ff2d	Moving CountTaxonOccurence.py	2025-01-08 10:38:23 -05:00
Adri K. Grow	a0b45ed2c8	Update CladeSizes.py ... Modified to work with clade grabbed input file names.	2024-11-11 08:59:47 -05:00
Auden Cote-L'Heureux	fb6e7aa6e7	Changing CladeGrabbing.py to use less than or equal to for number of contaminants	2024-11-01 10:34:57 -04:00
Katzlab	e2298810d2	Delete Utilities/for_trees/README.md	2024-08-09 10:04:55 -04:00
Adri K. Grow	b667dd6478	Update CountTaxonOccurence.py ... updated header	2024-08-07 18:16:01 -04:00
Katzlab	20e38f57b5	Update ColorByClade.py ... added example use and note on how to turn off rooting	2024-07-16 09:23:57 -04:00
Katzlab	6a86fded41	Update CountTaxonOccurence.py ... improving header	2024-06-09 13:02:38 -04:00
Katzlab	7aac410d85	Update CountTaxonOccurence.py ... adding option to look at only focal major clades	2024-06-09 13:01:59 -04:00
Katzlab	552e958952	Update CountTaxonOccurence.py ... updated to include summary of major and minor clades, and to allow target minor clade list	2024-06-09 12:44:26 -04:00
Katzlab	436cad7238	Purple color for EE	2024-06-06 17:23:26 -04:00
Godwin Ani	fd7b2e7302	rooting	2024-06-04 12:47:49 -04:00
Godwin Ani	f0799852b8	Update and rename RenameTips_v1.0.py to RenameTips.py	2024-06-03 16:07:31 -04:00
Godwin Ani	2635deefc1	Update and rename CountTaxonOccurence_v2.0.py to CountTaxonOccurence.py	2024-06-03 16:07:05 -04:00
Godwin Ani	81e5d5655e	Update and rename ContaminationBySisters_v2.2.py to ContaminationBySisters.py	2024-06-03 16:06:42 -04:00
Godwin Ani	a9ea2881be	Update and rename ColorByClade_v2.2.py to ColorByClade.py	2024-06-03 16:06:19 -04:00
Godwin Ani	6a9c37b71f	Update and rename CladeSizes_v2.0.py to CladeSizes.py	2024-06-03 16:06:00 -04:00
Godwin Ani	577e95d5e9	fix copying files twice	2024-06-03 16:05:35 -04:00
Godwin Ani	2a55025595	Delete Utilities/for_trees/ColorByClade_v3.2.py	2024-06-03 16:04:59 -04:00
Godwin Ani	c41de01a2c	Update and rename CladeGrabbing_v3.2.py to CladeGrabbing.py	2024-06-03 16:03:51 -04:00
Godwin Ani	160c4e58cc	Fix copying the files twice	2024-06-03 16:03:13 -04:00
Adri K. Grow	4f46d630dc	Update CladeGrabbing_v3.2.py	2024-06-03 14:50:00 -04:00
Godwin Ani	8b35b8a64d	Update CladeGrabbing_v3.2.py	2024-04-05 13:14:14 -04:00
Godwin Ani	5bdd2730bf	Rename CladeGrabbing_v2.1.py to CladeGrabbing_v3.2.py	2024-04-05 13:14:03 -04:00
Godwin Ani	e2134d08a3	New version	2024-04-05 13:13:23 -04:00
Godwin Ani	3f8bc48a3f	Update ColorByClade_v2.2.py	2024-04-01 11:11:06 -04:00
Godwin Ani	a59cbe1102	ColorByClade_v2.1.py to ColorByClade_v2.2.py	2024-04-01 11:10:18 -04:00
Godwin Ani	81a46d2714	Cannot set myself as outgroup catch	2024-04-01 11:09:45 -04:00
Katzlab	ca23f3f789	Update ColorByClade_v2.1.py ... undoing "fix" that was meant to allow you to color trees twice...	2024-02-20 16:48:44 -05:00
Auden Cote-L'Heureux	7ca7e378bc	Update ColorByClade_v2.1.py	2024-02-16 08:37:20 -05:00
Katzlab	710927f5fc	Update CladeGrabbing_v2.1.py	2024-02-14 17:46:48 -05:00
Godwin Ani	f6cb9e95ff	Update CountTaxonOccurence_v2.0.py	2024-02-05 13:53:22 -05:00
Godwin Ani	ded4143f11	Rename CladeSizes_v3.0.py to CladeSizes_v2.0.py	2024-02-05 13:51:38 -05:00
Katzlab	59b74bfa5f	Update CladeGrabbing_v2.1.py	2024-01-29 08:20:30 -05:00
Katzlab	719ce9bb9d	Added optional line to have keys WITHIN names rather than exclusively at start of name	2024-01-20 16:44:02 -05:00
Godwin Ani	dfa0f81763	Update and rename rename_tip_labels.py to RenameTips_v1.0.py	2024-01-15 15:00:53 -05:00
Godwin Ani	a25d0ac289	Rename CountTaxonOccurence.py to CountTaxonOccurence_v2.0.py	2024-01-15 15:00:07 -05:00
Auden Cote-L'Heureux	39a3ecb5d8	Changing default tip label font size	2023-12-22 12:00:21 -05:00
Auden Cote-L'Heureux	a53c89fdd7	Updating headers in CladeSizes_v3.0.py	2023-12-19 13:50:17 -05:00
Auden Cote-L'Heureux	d4aed039fd	Adding updated CladeSizes script with summary function	2023-12-19 13:49:49 -05:00
Auden Cote-L'Heureux	2688df4a98	Delete Utilities/for_trees/CladeSizes_v2.0.py	2023-12-19 13:49:13 -05:00
Auden Cote-L'Heureux	25b41672b3	Updating default colors in ColorByClade_v2.1.py	2023-12-18 11:21:49 -05:00
Auden Cote-L'Heureux	9cf716d431	Added clade-size (()()()) script	2023-12-01 12:15:21 -05:00
Auden Cote-L'Heureux	4e1ceae627	Delete Utilities/for_trees/ColorByClade_v2.0.py	2023-11-27 13:54:09 -05:00
Auden Cote-L'Heureux	3dd53c1eb9	Fixing rooting & ladderizing & node labels	2023-11-27 13:53:02 -05:00