MacOS software installation - Revision history

Gorm at 08:44, 19 March 2026

2026-03-19T08:44:54Z

← Older revision		Revision as of 10:44, 19 March 2026
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	install.packages("tidyverse")		install.packages("tidyverse")
	install.packages("bayesplot")		install.packages("bayesplot")
			install.packages("hexbin")

Gorm at 10:25, 11 February 2026

2026-02-11T10:25:06Z

← Older revision		Revision as of 12:25, 11 February 2026
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	; R, RStudio		; R, RStudio
	: Download newest version of R from [https://cran.rstudio.com CRAN] and follow instructions to install. Note: Different versions for Intel and Apple Silicon macs		* Download newest version of R from [https://cran.rstudio.com CRAN] and follow instructions to install. Note: Different versions for Intel and Apple Silicon macs
	: Download newest version of RStudio from [https://posit.co/download/rstudio-desktop/ posit.co] and follow instructions		* Download newest version of RStudio from [https://posit.co/download/rstudio-desktop/ posit.co] and follow instructions

	# R packages (do this inside Rstudio)		# R packages (do this inside Rstudio)
	install.packages("tidyverse")		install.packages("tidyverse")
	install.packages("bayesplot")		install.packages("bayesplot")

Gorm: /* Install required software */

2026-02-11T09:56:41Z

Install required software

← Older revision		Revision as of 11:56, 11 February 2026
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	== Install required software ==		== Install required software ==

			# Makes sure /usr/local/bin exists (won't overwrite it if it does)
			sudo mkdir -p /usr/local/bin

	# Homebrew: A package manager that can be used to more easily install other software		# Homebrew: A package manager that can be used to more easily install other software
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	# PAML		# PAML
	~~brew install brewsci~~/~~bio~~/paml		wget https://github.com/abacus-gene/paml/releases/download/v4.10.10/paml-4.10.10-mac-arm64.tar.gz
			tar -xvf paml-4.10.10-mac-arm64.tar.gz
			sudo cp paml-4.10.10-mac-arm64/bin/* /usr/local/bin
			rm -r paml-4.10.10-mac-arm64*

	# jmodeltest		# jmodeltest

Gorm at 10:56, 2 February 2026

2026-02-02T10:56:13Z

← Older revision		Revision as of 12:56, 2 February 2026
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	# FigTree		# FigTree
	~~brew install brewsci~~/~~bio~~/figtree		wget https://github.com/rambaut/figtree/releases/download/v1.4.4/FigTree.v1.4.4.dmg
			hdiutil mount FigTree.v1.4.4.dmg
			sudo cp -R "/Volumes/FigTree\ v1.4.4/FigTree\ v1.4.4.app" /Applications
			hdiutil unmount /Volumes/FigTree
			echo "alias figtree='open /Applications/FigTree\ v1.4.4.app'" >> ~/.zshrc

	# Tracer		# Tracer

Gorm at 10:49, 2 February 2026

2026-02-02T10:49:14Z

← Older revision		Revision as of 12:49, 2 February 2026
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	# BEASTX		# BEASTX
			brew install beagle
	brew install beast		brew install beast

Gorm at 10:34, 2 February 2026

2026-02-02T10:34:34Z

← Older revision		Revision as of 12:34, 2 February 2026
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	rm jmodeltest-2.1.10.tar.gz		rm jmodeltest-2.1.10.tar.gz
	echo "alias jmodeltest='java -jar /Applications/jmodeltest-2.1.10/jModelTest.jar &> /dev/null &'" >> ~/.zshrc		echo "alias jmodeltest='java -jar /Applications/jmodeltest-2.1.10/jModelTest.jar &> /dev/null &'" >> ~/.zshrc

			# BEASTX
			brew install beast

	# FigTree		# FigTree
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	# Activate changes to .rc file in current terminal session		# Activate changes to .rc file in current terminal session
	source ~/.zshrc		source ~/.zshrc

	~~; BEASTX~~
	~~: Download newest version of BEASTX from [https://beast.community BEASTX web site] and follow instructions to install.~~

	; R, RStudio		; R, RStudio

Gorm at 10:32, 2 February 2026

2026-02-02T10:32:45Z

← Older revision		Revision as of 12:32, 2 February 2026
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	# [https://github.com/agormp/phylotreelib GitHub phylotreelib] [https://github.com/agormp/seqconverter GitHub seqconverter] [https://github.com/agormp/sumt GitHub sumt]		# [https://github.com/agormp/phylotreelib GitHub phylotreelib] [https://github.com/agormp/seqconverter GitHub seqconverter] [https://github.com/agormp/sumt GitHub sumt]
	# These instructions assume you already have a working installation of python3		# These instructions assume you already have a working installation of python3
			python3 -m ensurepip --upgrade
	python3 -m pip install seqconverter		python3 -m pip install seqconverter
	python3 -m pip install phylotreelib		python3 -m pip install phylotreelib

Gorm at 10:17, 2 February 2026

2026-02-02T10:17:04Z

← Older revision		Revision as of 12:17, 2 February 2026
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	# Note: This only works if java has access to files and folders on the mac		# Note: This only works if java has access to files and folders on the mac
	wget https://ormbunkar.se/aliview/downloads/mac/AliView-1.30-app.zip		wget https://ormbunkar.se/aliview/downloads/mac/AliView-1.30-app.zip
	unzip AliView-1.28-app.zip		unzip AliView-1.30-app.zip
	sudo mv AliView-1.28/AliView.app /Applications		sudo mv AliView-1.30/AliView.app /Applications
	rm -r AliView-1.28		rm -r AliView-1.30
	echo 'aliview() { java -jar /Applications/AliView.app/Contents/Resources/Java/repo/AliView/AliView/1.28/AliView-1.28.jar "$1" &> /dev/null & }' >> ~/.zshrc		echo 'aliview() { java -jar /Applications/AliView.app/Contents/Resources/Java/repo/AliView/AliView/1.30/AliView-1.30.jar "$1" &> /dev/null & }' >> ~/.zshrc

	# Anders Gorm software: seqconverter, phylotreelib, sumt		# Anders Gorm software: seqconverter, phylotreelib, sumt

Gorm at 10:10, 2 February 2026

2026-02-02T10:10:51Z

← Older revision		Revision as of 12:10, 2 February 2026
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	== Install required software ==		== Install required software ==

	# Homebrew		# Homebrew: A package manager that can be used to more easily install other software
	xcode-select --install		xcode-select --install
	/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"		/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"

	Note: for the one-liner installation of home-brew above, [https://docs.brew.sh/Installation you need to use /bin/bash when installing, even if your shell is zsh].		Note: for the one-liner installation of home-brew above, [https://docs.brew.sh/Installation you need to use /bin/bash when installing, even if your shell is zsh].

			# wget: command-line tool for downloading files from the internet
			brew install wget

	# Text editor		# Text editor
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	sudo tar -xvf jmodeltest-2.1.10.tar.gz --directory /Applications		sudo tar -xvf jmodeltest-2.1.10.tar.gz --directory /Applications
	rm jmodeltest-2.1.10.tar.gz		rm jmodeltest-2.1.10.tar.gz
	echo "alias jmodeltest='java -jar /Applications/jmodeltest-2.1.10/jModelTest.jar &> /dev/null &'" >> .zshrc		echo "alias jmodeltest='java -jar /Applications/jmodeltest-2.1.10/jModelTest.jar &> /dev/null &'" >> ~/.zshrc

	# FigTree		# FigTree
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	sudo cp -R "/Volumes/Tracer/Tracer v1.7.2.app" /Applications		sudo cp -R "/Volumes/Tracer/Tracer v1.7.2.app" /Applications
	hdiutil unmount /Volumes/Tracer		hdiutil unmount /Volumes/Tracer
	echo "alias tracer='open /Applications/Tracer\ v1.7.2.app'" >> .zshrc		echo "alias tracer='open /Applications/Tracer\ v1.7.2.app'" >> ~/.zshrc

	# TempEst		# TempEst
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	sudo tar -zxf TempEst_v1.5.3.tgz --directory /Applications		sudo tar -zxf TempEst_v1.5.3.tgz --directory /Applications
	sudo chmod 755 /Applications/TempEst_v1.5.3/bin/tempest		sudo chmod 755 /Applications/TempEst_v1.5.3/bin/tempest
	echo "alias tempest='/Applications/TempEst_v1.5.3/bin/tempest'" >> .zshrc		echo "alias tempest='/Applications/TempEst_v1.5.3/bin/tempest'" >> ~/.zshrc
	rm TempEst_v1.5.3.tgz		rm TempEst_v1.5.3.tgz

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	sudo mv AliView-1.28/AliView.app /Applications		sudo mv AliView-1.28/AliView.app /Applications
	rm -r AliView-1.28		rm -r AliView-1.28
	echo 'aliview() { java -jar /Applications/AliView.app/Contents/Resources/Java/repo/AliView/AliView/1.28/AliView-1.28.jar "$1" &> /dev/null & }' >> .zshrc		echo 'aliview() { java -jar /Applications/AliView.app/Contents/Resources/Java/repo/AliView/AliView/1.28/AliView-1.28.jar "$1" &> /dev/null & }' >> ~/.zshrc

	# Anders Gorm software: seqconverter, phylotreelib, sumt		# Anders Gorm software: seqconverter, phylotreelib, sumt
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	# Activate changes to .rc file in current terminal session		# Activate changes to .rc file in current terminal session
	source .zshrc		source ~/.zshrc

	; BEASTX		; BEASTX

Gorm at 12:43, 31 January 2026

2026-01-31T12:43:48Z

← Older revision		Revision as of 14:43, 31 January 2026
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	chmod 755 paup4a168_osx		chmod 755 paup4a168_osx
	sudo mv paup4a168_osx /usr/local/bin/paup		sudo mv paup4a168_osx /usr/local/bin/paup

			# IQ-TREE 3
			brew install brewsci/bio/iqtree3

	# PAML		# PAML
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	hdiutil unmount /Volumes/Tracer		hdiutil unmount /Volumes/Tracer
	echo "alias tracer='open /Applications/Tracer\ v1.7.2.app'" >> .zshrc		echo "alias tracer='open /Applications/Tracer\ v1.7.2.app'" >> .zshrc

			# TempEst
			wget --content-disposition 'https://tree.bio.ed.ac.uk/download.php?id=102&num=3'
			sudo tar -zxf TempEst_v1.5.3.tgz --directory /Applications
			sudo chmod 755 /Applications/TempEst_v1.5.3/bin/tempest
			echo "alias tempest='/Applications/TempEst_v1.5.3/bin/tempest'" >> .zshrc
			rm TempEst_v1.5.3.tgz

	# MAFFT		# MAFFT
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	echo 'aliview() { java -jar /Applications/AliView.app/Contents/Resources/Java/repo/AliView/AliView/1.28/AliView-1.28.jar "$1" &> /dev/null & }' >> .zshrc		echo 'aliview() { java -jar /Applications/AliView.app/Contents/Resources/Java/repo/AliView/AliView/1.28/AliView-1.28.jar "$1" &> /dev/null & }' >> .zshrc

	# seqconverter, ~~sequencelib~~, ~~phylotreelib~~		# Anders Gorm software: seqconverter, phylotreelib, sumt
	# These are scripts and libraries written by me:		# These are scripts and libraries written by me:
	# [https://github.com/agormp/phylotreelib GitHub phylotreelib] [https://github.com/agormp/~~sequencelib~~ GitHub ~~sequencelib~~] [https://github.com/agormp/~~seqconverter~~ GitHub ~~seqconverter~~]		# [https://github.com/agormp/phylotreelib GitHub phylotreelib] [https://github.com/agormp/seqconverter GitHub seqconverter] [https://github.com/agormp/sumt GitHub sumt]
	# These instructions assume you already have a working installation of python3		# These instructions assume you already have a working installation of python3
	python3 -m pip install seqconverter		python3 -m pip install seqconverter
	python3 -m pip install phylotreelib		python3 -m pip install phylotreelib
			python3 -m pip install sumt

	# maxalign tool		# maxalign tool
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	source .zshrc		source .zshrc

	; ~~BEAST2~~		; BEASTX
	: Download newest version of ~~BEAST2~~ from [https://~~www~~.~~beast2.org BEAST2~~ web site] and follow instructions to install.		: Download newest version of BEASTX from [https://beast.community BEASTX web site] and follow instructions to install.
	~~<!--~~
	~~# BEAST2~~
	~~brew install beast2~~
	~~echo 'PATH="/usr/local/opt/beast2/libexec/bin${PATH:+:${PATH}}"' >> .zshrc~~
	~~-->~~

	; R, RStudio		; R, RStudio
	: Download newest version of R from [https://~~mirrors~~.~~dotsrc~~.~~org/cran/~~ CRAN] and follow instructions to install. Note: Different versions for Intel and Apple Silicon macs		: Download newest version of R from [https://cran.rstudio.com CRAN] and follow instructions to install. Note: Different versions for Intel and Apple Silicon macs
	: Download newest version of RStudio from [https://posit.co/download/rstudio-desktop/~~#download~~ posit.co] and follow instructions		: Download newest version of RStudio from [https://posit.co/download/rstudio-desktop/ posit.co] and follow instructions

	# R packages (do this inside Rstudio)		# R packages (do this inside Rstudio)
	install.packages("tidyverse")		install.packages("tidyverse")
	install.packages("bayesplot")		install.packages("bayesplot")