Code

Version 3.8 release#106

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Merged

wmaddisn merged 68 commits intomasterMesquiteProject/MesquiteCore:masterfrom developmentMesquiteProject/MesquiteCore:developmentCopy head branch name to clipboardApr 10, 2023

+3,795-514

Commits

Commits on Aug 27, 2021

• Prerelease

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Commits on Sep 20, 2021

• Clean up bogus carriage returns

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Commits on Feb 7, 2022

• BLAST log adjustment

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Commits on May 9, 2022

• Use commons-text

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• Remove redundant IDs in taxon

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• Minor comment

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Commits on May 10, 2022

• Switch LocalBlaster to use ExternalProcessManager

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• Build number

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• Specification of BLAST exec dir

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Commits on May 11, 2022

• Allowing custom BLAST database location

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Commits on May 12, 2022

• Manual updates

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Commits on Aug 30, 2022

• Add DeleteCharsByGBLOCKS module

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• Suppressed repeated recalculations when rows of list window are deleted.

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Commits on Aug 31, 2022

• Adding to Resources so that default Mesquite_Folder is executable

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• Fixing placement of Resources and jars

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Commits on Sep 18, 2022

• Fix cast exception.

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Commits on Nov 3, 2022

• Debugmode contradict clade list

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• Build number

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Commits on Dec 10, 2022

• Allow user to enter * for file list

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• Minor boolean addition

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Commits on Jan 17, 2023

• Updated voucher info for Chromaseq

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Commits on Feb 8, 2023

• Added ResolveDNAAmbiguities

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Commits on Feb 18, 2023

• NPE protection in StringUtil

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• InterpretPhylip option to not write empty characters

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• partial InterpretFasta support for writeCharactersWithNoData

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• Build update

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Commits on Mar 19, 2023

• Added InterpretFastaDNAbyOTUID

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Commits on Mar 24, 2023

• Added ExportForBEAST

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Commits on Mar 25, 2023

• changed package name from mb to bayesian

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• removed commented-out code

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Commits on Mar 26, 2023

• Fixed TaxSet export, added duplicates

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• Added Export BEAST to new features doc

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• Removed taxon set duplication BEAST export

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Commits on Mar 29, 2023

• Prep for RAxML-NG

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Commits on Mar 30, 2023

• Corrections for RAxML models

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Commits on Apr 3, 2023

• Mark ResolveDNAAmbig as not prerelease

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Commits on Apr 8, 2023

• ListableVector notification of change adjusted

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• Add warning query if multiple matrices to be duplicated.

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• trying again to push

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Commits on Apr 9, 2023

• New module to export taxa as separate fasta files

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• docs addition about new module (export separate fastas)

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• Remove duplicatetaxonnames BEAST2

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• Tidying up new modules

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• Fixed NEXTRELEASE

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• Merge branch 'development' of https://github.com/MesquiteProject/MesquiteCore into development

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• Doc update

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• More work on History of New Features doc

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• Docs and strings updated to 3.80 and 2023

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• FlipTaxonLocus

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• Merge branch 'development' of

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• FlipTaxon revise, fix NPE in Ext.Proc.Man

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• Flip 3

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• Flip 4

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• Flip 5

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• Flip 6

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Commits on Apr 10, 2023

• removeQuotes from StringArray

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• Quotes around .py path

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• Flip 7

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• Cleaned up Flip

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• Fixing version numbers etc. in Mesquite.java

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• launch4j deleted (temporarily?)

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• added isPrerelease

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• Change default BLAST files to *

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• Merge branch 'development' of https://github.com/MesquiteProject/MesquiteCore into development

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• Docs updating. Recovering deleted launch4j folder.

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• Build number change

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• doc updates

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• notices.xml updated.

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